Psyllid ID: psy6372

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------
Protein Sequence
MSTPLPCNPKPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTGKLGEVLIRCNNILYIRGAEEGDEEGEMRE
Secondary Structure (PSIPRED)
cccccccccHHHHHHccccEEEEEEcccEEEEEEEEEEEcEEEEEEccEEEEEccEEccccccEEEEcccEEEEEccccccccccccc
Secondary Structure Prediction (SSPRO)
cccccccccHHHHHHHcccEEEEEEcccEEEEEEEEEEcccccEEEEEEEEEEccEEEEEEEEEEEcHHHEEEEEccccccccccccc
Coil and Loop (DISEMBL)
mstplpcnpkpflnlltgksvicklkwgheykgilvstdgymncqlasteeiidghctGKLGEVLIRCNNILyirgaeegdeegemre
Flexible Loop (DISEMBL)
mstplpcnpkpflnLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTGKLGEVLIRCNNIlyirgaeegdeegemre
Low Complexity Region (SEG)
MSTPLPCNPKPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTGKLGEVLIRCNNILYIRgaeegdeegemre
Disordered region (IsUnstruct)
**********PFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTGKLGEVLIRCNNILYIRG************
Disordered Region (DISOPRED)
******C***PFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTGKLGEVLIRCNNILYI**************
Disordered Region (DISEMBL)
MSTPLPCNPKPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTGKLGEVLIRCNNILYIRGAE**********
Disordered Region (DISPRO)
*****PCNPKPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTGKLGEVLIRCNNILYIRGAE**********
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
oooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhooooooooooooo
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Signal Peptide (SignalP NN Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Coiled Coils (COILS)
MSTPLPCNPKPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTGKLGEVLIRCNNILYIRGAEEGDEEGEMRE
Positional Conservation
no confident homologs detected

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Close Homologs for Annotation Transfer

Close Homologs in SWISS-PROT Database Detected by BLAST

Original result of BLAST against SWISS-PROT Database

ID	Length	Definition	RBH(Q2H)	RBH(H2Q)	Q cover	H cover	Identity	E-value
Query	88	2.2.26 [Sep-21-2011]
Q24297	88	Small nuclear ribonucleop	yes	N/A	1.0	1.0	0.727	8e-33
Q9SUM2	88	Probable small nuclear ri	yes	N/A	0.886	0.886	0.692	4e-27
P62321	86	Small nuclear ribonucleop	N/A	N/A	0.829	0.848	0.767	2e-26
P62307	86	Small nuclear ribonucleop	yes	N/A	0.829	0.848	0.767	2e-26
P62306	86	Small nuclear ribonucleop	yes	N/A	0.829	0.848	0.767	2e-26
Q3T0Z8	86	Small nuclear ribonucleop	yes	N/A	0.829	0.848	0.767	2e-26
P34659	85	Probable small nuclear ri	yes	N/A	0.931	0.964	0.646	5e-26
O59734	78	Small nuclear ribonucleop	yes	N/A	0.795	0.897	0.614	1e-20
Q54XP2	91	Small nuclear ribonucleop	yes	N/A	0.897	0.868	0.587	4e-20
Q9P5Z8	90	Probable small nuclear ri	N/A	N/A	0.943	0.922	0.523	6e-20

>sp|Q24297|RUXF_DROME Small nuclear ribonucleoprotein F OS=Drosophila melanogaster GN=SmF PE=3 SV=2

 Score =  138 bits (348), Expect = 8e-33,   Method: Compositional matrix adjust.
 Identities = 64/88 (72%), Positives = 73/88 (82%)

Query: 1  MSTPLPCNPKPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTGK 60
          MS  +P NPKPFLN LTGK V+ KLKWG EYKG LVS DGYMN QLA+TEE+I+G  TG 
Sbjct: 1  MSAGMPINPKPFLNGLTGKPVLVKLKWGQEYKGFLVSVDGYMNMQLANTEEVIEGSVTGN 60

Query: 61 LGEVLIRCNNILYIRGAEEGDEEGEMRE 88
          LGEVLIRCNN+LYI+G E+ DEEGEMR+
Sbjct: 61 LGEVLIRCNNVLYIKGMEDDDEEGEMRD 88

Associated with snRNP U1, U2, U4/U6 and U5.
Drosophila melanogaster (taxid: 7227)

>sp|Q9SUM2|RUXF_ARATH Probable small nuclear ribonucleoprotein F OS=Arabidopsis thaliana GN=At4g30220 PE=2 SV=1

 Score =  119 bits (299), Expect = 4e-27,   Method: Compositional matrix adjust.
 Identities = 54/78 (69%), Positives = 61/78 (78%)

Query: 5  LPCNPKPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTGKLGEV 64
          +P NPKPFLN LTGK+VI KLKWG EYKG L S D YMN QL +TEE IDG  TG LGE+
Sbjct: 4  IPVNPKPFLNNLTGKTVIVKLKWGMEYKGFLASVDSYMNLQLGNTEEYIDGQLTGNLGEI 63

Query: 65 LIRCNNILYIRGAEEGDE 82
          LIRCNN+LY+RG  E +E
Sbjct: 64 LIRCNNVLYVRGVPEDEE 81

Probable common Sm protein, is found in U1 and U2 snRNPs.

Arabidopsis thaliana (taxid: 3702)

>sp|P62321|RUXF_XENLA Small nuclear ribonucleoprotein F OS=Xenopus laevis GN=snrpf PE=3 SV=1

 Score =  117 bits (293), Expect = 2e-26,   Method: Compositional matrix adjust.
 Identities = 56/73 (76%), Positives = 60/73 (82%)

Query: 5  LPCNPKPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTGKLGEV 64
          LP NPKPFLN LTGK V+ KLKWG EYKG LVS DGYMN QLA+TEE IDG  +G LGEV
Sbjct: 3  LPLNPKPFLNGLTGKPVMVKLKWGMEYKGYLVSVDGYMNMQLANTEEYIDGALSGHLGEV 62

Query: 65 LIRCNNILYIRGA 77
          LIRCNN+LYIRG 
Sbjct: 63 LIRCNNVLYIRGV 75

Appears to function in the U7 snRNP complex that is involved in histone 3'-end processing. Associated with snRNP U1, U2, U4/U6 and U5.

Xenopus laevis (taxid: 8355)

>sp|P62307|RUXF_MOUSE Small nuclear ribonucleoprotein F OS=Mus musculus GN=Snrpf PE=2 SV=1

 Score =  117 bits (293), Expect = 2e-26,   Method: Compositional matrix adjust.
 Identities = 56/73 (76%), Positives = 60/73 (82%)

Query: 5  LPCNPKPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTGKLGEV 64
          LP NPKPFLN LTGK V+ KLKWG EYKG LVS DGYMN QLA+TEE IDG  +G LGEV
Sbjct: 3  LPLNPKPFLNGLTGKPVMVKLKWGMEYKGYLVSVDGYMNMQLANTEEYIDGALSGHLGEV 62

Query: 65 LIRCNNILYIRGA 77
          LIRCNN+LYIRG 
Sbjct: 63 LIRCNNVLYIRGV 75

Appears to function in the U7 snRNP complex that is involved in histone 3'-end processing. Associated with snRNP U1, U2, U4/U6 and U5.

Mus musculus (taxid: 10090)

>sp|P62306|RUXF_HUMAN Small nuclear ribonucleoprotein F OS=Homo sapiens GN=SNRPF PE=1 SV=1

 Score =  117 bits (293), Expect = 2e-26,   Method: Compositional matrix adjust.
 Identities = 56/73 (76%), Positives = 60/73 (82%)

Query: 5  LPCNPKPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTGKLGEV 64
          LP NPKPFLN LTGK V+ KLKWG EYKG LVS DGYMN QLA+TEE IDG  +G LGEV
Sbjct: 3  LPLNPKPFLNGLTGKPVMVKLKWGMEYKGYLVSVDGYMNMQLANTEEYIDGALSGHLGEV 62

Query: 65 LIRCNNILYIRGA 77
          LIRCNN+LYIRG 
Sbjct: 63 LIRCNNVLYIRGV 75

Appears to function in the U7 snRNP complex that is involved in histone 3'-end processing. Associated with snRNP U1, U2, U4/U6 and U5.

Homo sapiens (taxid: 9606)

>sp|Q3T0Z8|RUXF_BOVIN Small nuclear ribonucleoprotein F OS=Bos taurus GN=SNRPF PE=3 SV=2

 Score =  117 bits (293), Expect = 2e-26,   Method: Compositional matrix adjust.
 Identities = 56/73 (76%), Positives = 60/73 (82%)

Query: 5  LPCNPKPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTGKLGEV 64
          LP NPKPFLN LTGK V+ KLKWG EYKG LVS DGYMN QLA+TEE IDG  +G LGEV
Sbjct: 3  LPLNPKPFLNGLTGKPVMVKLKWGMEYKGYLVSVDGYMNMQLANTEEYIDGALSGHLGEV 62

Query: 65 LIRCNNILYIRGA 77
          LIRCNN+LYIRG 
Sbjct: 63 LIRCNNVLYIRGV 75

Appears to function in the U7 snRNP complex that is involved in histone 3'-end processing. Associated with snRNP U1, U2, U4/U6 and U5.

Bos taurus (taxid: 9913)

>sp|P34659|RUXF_CAEEL Probable small nuclear ribonucleoprotein F OS=Caenorhabditis elegans GN=snr-5 PE=1 SV=1

 Score =  116 bits (290), Expect = 5e-26,   Method: Compositional matrix adjust.
 Identities = 53/82 (64%), Positives = 62/82 (75%)

Query: 1  MSTPLPCNPKPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTGK 60
          MS   P NPKPFLN LTGK V+CKLKWG EYKG+LV+ D YMN QLA  EE IDG+  G 
Sbjct: 1  MSAVQPVNPKPFLNSLTGKFVVCKLKWGMEYKGVLVAVDSYMNLQLAHAEEYIDGNSQGN 60

Query: 61 LGEVLIRCNNILYIRGAEEGDE 82
          LGE+LIRCNN+LY+ G +  +E
Sbjct: 61 LGEILIRCNNVLYVGGVDGENE 82

Associated with snRNP U1, U2, U4/U6 and U5.

Caenorhabditis elegans (taxid: 6239)

>sp|O59734|RUXF_SCHPO Small nuclear ribonucleoprotein F OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=smf1 PE=1 SV=1

 Score = 98.2 bits (243), Expect = 1e-20,   Method: Compositional matrix adjust.
 Identities = 43/70 (61%), Positives = 53/70 (75%)

Query: 5  LPCNPKPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTGKLGEV 64
          +P NPKPFL  L GK V+ +LKWG EYKG L S D YMN QL + EE++DG  TG LGE+
Sbjct: 4  VPVNPKPFLQGLIGKPVLVRLKWGQEYKGTLQSVDSYMNLQLLNAEELVDGVKTGDLGEI 63

Query: 65 LIRCNNILYI 74
          LIRCNN+L++
Sbjct: 64 LIRCNNVLWV 73

Involved in pre-mRNA splicing. Binds snRNA U1, U2, U4 and U5 which contain a highly conserved structural motif called the Sm binding site.

Schizosaccharomyces pombe (strain 972 / ATCC 24843) (taxid: 284812)

>sp|Q54XP2|RUXF_DICDI Small nuclear ribonucleoprotein F OS=Dictyostelium discoideum GN=snrpf PE=3 SV=1

 Score = 96.7 bits (239), Expect = 4e-20,   Method: Compositional matrix adjust.
 Identities = 47/80 (58%), Positives = 56/80 (70%), Gaps = 1/80 (1%)

Query: 1  MSTPLPCNPKPFLNLLTGKSVICKLKWG-HEYKGILVSTDGYMNCQLASTEEIIDGHCTG 59
          MS      PKPFL  L GK +  +LKWG  EY+GIL S D YMN QLA+TEE IDG   G
Sbjct: 1  MSKIEALAPKPFLYDLKGKKIAVRLKWGGMEYRGILASVDSYMNLQLAATEEWIDGANKG 60

Query: 60 KLGEVLIRCNNILYIRGAEE 79
           LGEVLIRCNN+L++RG ++
Sbjct: 61 PLGEVLIRCNNVLFVRGIDD 80

Associated with snRNP U1, U2, U4/U6 and U5.

Dictyostelium discoideum (taxid: 44689)

>sp|Q9P5Z8|RUXF_NEUCR Probable small nuclear ribonucleoprotein F OS=Neurospora crassa (strain ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987) GN=B2O8.190 PE=3 SV=1

 Score = 95.9 bits (237), Expect = 6e-20,   Method: Compositional matrix adjust.
 Identities = 44/84 (52%), Positives = 58/84 (69%), Gaps = 1/84 (1%)

Query: 5  LPCNPKPFLNLLTGKSVICKLKWGH-EYKGILVSTDGYMNCQLASTEEIIDGHCTGKLGE 63
          +P NP+PFL  L    V  +LKWG  EY G LVS D YMN QL+ T+E I+   TG LG+
Sbjct: 4  VPVNPRPFLQDLVNSFVTIRLKWGETEYVGRLVSIDSYMNIQLSDTKEYINRKFTGALGQ 63

Query: 64 VLIRCNNILYIRGAEEGDEEGEMR 87
          VLIRCNN+LYI+ A+E +  G+++
Sbjct: 64 VLIRCNNVLYIKKADEAETSGDVK 87

Probable common Sm protein, is found in U1 and U2 snRNPs.

Neurospora crassa (strain ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987) (taxid: 367110)

Close Homologs in the Non-Redundant Database Detected by BLAST

Original result of BLAST against Nonredundant Database

GI	Length	Definition	Q cover	H cover	Identity	E-value
Query	88
290561351	86	Small nuclear ribonucleoprotein F [Lepeo	0.954	0.976	0.785	1e-32
31212897	88	AGAP002658-PA [Anopheles gambiae str. PE	1.0	1.0	0.75	2e-32
170032813	88	small nuclear ribonucleoprotein F [Culex	1.0	1.0	0.738	4e-32
312371148	88	hypothetical protein AND_30966 [Anophele	1.0	1.0	0.738	4e-32
225709496	86	Small nuclear ribonucleoprotein F [Calig	0.954	0.976	0.761	7e-32
332031555	88	Small nuclear ribonucleoprotein F [Acrom	1.0	1.0	0.738	9e-32
307186677	84	Small nuclear ribonucleoprotein F [Campo	0.954	1.0	0.773	3e-31
22024001	88	small ribonucleoprotein particle protein	1.0	1.0	0.727	3e-31
153792507	88	small nuclear ribonucleoprotein protein	0.886	0.886	0.769	3e-30
357605279	88	small nuclear ribonucleoprotein F [Danau	0.875	0.875	0.766	1e-29

>gi|290561351|gb|ADD38076.1| Small nuclear ribonucleoprotein F [Lepeophtheirus salmonis]

 Score =  143 bits (361), Expect = 1e-32,   Method: Compositional matrix adjust.
 Identities = 66/84 (78%), Positives = 74/84 (88%)

Query: 5  LPCNPKPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTGKLGEV 64
          +P NPKPFLN LTGK+V+ KLKWGHEYKG LVSTDGYMN QLA+TEE IDG+CTG LGEV
Sbjct: 3  MPINPKPFLNELTGKAVMVKLKWGHEYKGYLVSTDGYMNVQLANTEEYIDGNCTGTLGEV 62

Query: 65 LIRCNNILYIRGAEEGDEEGEMRE 88
          L+RCNN+LYIRG +E DEEGE RE
Sbjct: 63 LVRCNNVLYIRGVQEDDEEGETRE 86

Source: Lepeophtheirus salmonis

Species: Lepeophtheirus salmonis

Genus: Lepeophtheirus

Family: Caligidae

Order: Siphonostomatoida

Class: Maxillopoda

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|31212897|ref|XP_312266.1| AGAP002658-PA [Anopheles gambiae str. PEST] gi|30177439|gb|EAA07677.2| AGAP002658-PA [Anopheles gambiae str. PEST]

 Score =  142 bits (359), Expect = 2e-32,   Method: Compositional matrix adjust.
 Identities = 66/88 (75%), Positives = 74/88 (84%)

Query: 1  MSTPLPCNPKPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTGK 60
          M+T +P NPKPFLN LTGK VI KLKWGHEYKG LVS DGYMN QLA+TEE +DG  TG 
Sbjct: 1  MTTAMPINPKPFLNGLTGKPVIIKLKWGHEYKGFLVSVDGYMNMQLANTEEFVDGQNTGH 60

Query: 61 LGEVLIRCNNILYIRGAEEGDEEGEMRE 88
          LGEVLIRCNN+LYIRG ++ DEEGEMR+
Sbjct: 61 LGEVLIRCNNVLYIRGIDDEDEEGEMRD 88

Source: Anopheles gambiae str. PEST

Species: Anopheles gambiae

Genus: Anopheles

Family: Culicidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|170032813|ref|XP_001844274.1| small nuclear ribonucleoprotein F [Culex quinquefasciatus] gi|167873231|gb|EDS36614.1| small nuclear ribonucleoprotein F [Culex quinquefasciatus]

 Score =  141 bits (356), Expect = 4e-32,   Method: Compositional matrix adjust.
 Identities = 65/88 (73%), Positives = 74/88 (84%)

Query: 1  MSTPLPCNPKPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTGK 60
          M+T +P NPKPFLN LTGK VI KLKWGHEYKG LVS DGYMN QLA+T+E +DG  TG 
Sbjct: 1  MTTAMPINPKPFLNGLTGKPVIIKLKWGHEYKGFLVSVDGYMNMQLANTDEYVDGQNTGH 60

Query: 61 LGEVLIRCNNILYIRGAEEGDEEGEMRE 88
          LGEVLIRCNN+LYIRG ++ DEEGEMR+
Sbjct: 61 LGEVLIRCNNVLYIRGIDDDDEEGEMRD 88

Source: Culex quinquefasciatus

Species: Culex quinquefasciatus

Genus: Culex

Family: Culicidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|312371148|gb|EFR19407.1| hypothetical protein AND_30966 [Anopheles darlingi]

 Score =  141 bits (356), Expect = 4e-32,   Method: Compositional matrix adjust.
 Identities = 65/88 (73%), Positives = 74/88 (84%)

Query: 1  MSTPLPCNPKPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTGK 60
          M+T +P NPKPFLN LTGK V+ KLKWGHEYKG LVS DGYMN QLA+TEE +DG  TG 
Sbjct: 1  MATAMPINPKPFLNGLTGKPVMIKLKWGHEYKGFLVSVDGYMNMQLANTEEFVDGQNTGH 60

Query: 61 LGEVLIRCNNILYIRGAEEGDEEGEMRE 88
          LGEVLIRCNN+LYIRG ++ DEEGEMR+
Sbjct: 61 LGEVLIRCNNVLYIRGIDDEDEEGEMRD 88

Source: Anopheles darlingi

Species: Anopheles darlingi

Genus: Anopheles

Family: Culicidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|225709496|gb|ACO10594.1| Small nuclear ribonucleoprotein F [Caligus rogercresseyi]

 Score =  140 bits (354), Expect = 7e-32,   Method: Compositional matrix adjust.
 Identities = 64/84 (76%), Positives = 74/84 (88%)

Query: 5  LPCNPKPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTGKLGEV 64
          +P NPKPFLN LTGK+V+ KLKWGHEYKG LVS+DGYMN QLA+TEE IDG+CTG LGEV
Sbjct: 3  MPINPKPFLNELTGKAVMVKLKWGHEYKGYLVSSDGYMNVQLANTEEYIDGNCTGTLGEV 62

Query: 65 LIRCNNILYIRGAEEGDEEGEMRE 88
          L+RCNN+LYIRG +E DEEGE +E
Sbjct: 63 LVRCNNVLYIRGVQEDDEEGETKE 86

Source: Caligus rogercresseyi

Species: Caligus rogercresseyi

Genus: Caligus

Family: Caligidae

Order: Siphonostomatoida

Class: Maxillopoda

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|332031555|gb|EGI71027.1| Small nuclear ribonucleoprotein F [Acromyrmex echinatior]

 Score =  140 bits (353), Expect = 9e-32,   Method: Compositional matrix adjust.
 Identities = 65/88 (73%), Positives = 75/88 (85%)

Query: 1  MSTPLPCNPKPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTGK 60
          M+  +P NPKPFLN LTGK V+ KLKWGHEYKG LVS DGYMN QLA+TEE I+G+CTG 
Sbjct: 1  MAATMPINPKPFLNGLTGKPVMVKLKWGHEYKGYLVSVDGYMNLQLANTEEHIEGNCTGN 60

Query: 61 LGEVLIRCNNILYIRGAEEGDEEGEMRE 88
          LGEVLIRCNN++YIRG EE DEEGEM++
Sbjct: 61 LGEVLIRCNNVMYIRGVEESDEEGEMKD 88

Source: Acromyrmex echinatior

Species: Acromyrmex echinatior

Genus: Acromyrmex

Family: Formicidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|307186677|gb|EFN72155.1| Small nuclear ribonucleoprotein F [Camponotus floridanus]

 Score =  139 bits (349), Expect = 3e-31,   Method: Compositional matrix adjust.
 Identities = 65/84 (77%), Positives = 72/84 (85%)

Query: 5  LPCNPKPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTGKLGEV 64
          +P NPKPFLN LTGK V+ KLKWGHEYKG LVS DGYMN QLA+TEE IDG CTG LGEV
Sbjct: 1  MPINPKPFLNGLTGKPVMVKLKWGHEYKGYLVSVDGYMNLQLANTEEHIDGSCTGNLGEV 60

Query: 65 LIRCNNILYIRGAEEGDEEGEMRE 88
          LIRCNN++YIRG EE DEEGEM++
Sbjct: 61 LIRCNNVMYIRGVEESDEEGEMKD 84

Source: Camponotus floridanus

Species: Camponotus floridanus

Genus: Camponotus

Family: Formicidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|22024001|ref|NP_523708.2| small ribonucleoprotein particle protein SmF [Drosophila melanogaster] gi|125807333|ref|XP_001360364.1| GA14154 [Drosophila pseudoobscura pseudoobscura] gi|194754150|ref|XP_001959360.1| GF12081 [Drosophila ananassae] gi|194883764|ref|XP_001975970.1| GG22599 [Drosophila erecta] gi|195056665|ref|XP_001995140.1| GH22983 [Drosophila grimshawi] gi|195122320|ref|XP_002005660.1| GI18952 [Drosophila mojavensis] gi|195149774|ref|XP_002015830.1| GL11267 [Drosophila persimilis] gi|195333646|ref|XP_002033498.1| GM20378 [Drosophila sechellia] gi|195381309|ref|XP_002049395.1| GJ21558 [Drosophila virilis] gi|195436262|ref|XP_002066088.1| GK22120 [Drosophila willistoni] gi|195485487|ref|XP_002091113.1| GE13467 [Drosophila yakuba] gi|195551853|ref|XP_002076311.1| GD15243 [Drosophila simulans] gi|195551862|ref|XP_002076315.1| DebB [Drosophila simulans] gi|29337191|sp|Q24297.2|RUXF_DROME RecName: Full=Small nuclear ribonucleoprotein F; Short=snRNP-F; AltName: Full=Membrane-associated protein Deb-B; AltName: Full=Sm protein F; Short=Sm-F; Short=SmF gi|21430088|gb|AAM50722.1| GM23968p [Drosophila melanogaster] gi|21645477|gb|AAF58559.2| small ribonucleoprotein particle protein SmF [Drosophila melanogaster] gi|54635536|gb|EAL24939.1| GA14154 [Drosophila pseudoobscura pseudoobscura] gi|190620658|gb|EDV36182.1| GF12081 [Drosophila ananassae] gi|190659157|gb|EDV56370.1| GG22599 [Drosophila erecta] gi|193899346|gb|EDV98212.1| GH22983 [Drosophila grimshawi] gi|193910728|gb|EDW09595.1| GI18952 [Drosophila mojavensis] gi|194109677|gb|EDW31720.1| GL11267 [Drosophila persimilis] gi|194125468|gb|EDW47511.1| GM20378 [Drosophila sechellia] gi|194144192|gb|EDW60588.1| GJ21558 [Drosophila virilis] gi|194162173|gb|EDW77074.1| GK22120 [Drosophila willistoni] gi|194177214|gb|EDW90825.1| GE13467 [Drosophila yakuba] gi|194201960|gb|EDX15536.1| GD15243 [Drosophila simulans] gi|194201964|gb|EDX15540.1| DebB [Drosophila simulans] gi|220956990|gb|ACL91038.1| DebB-PA [synthetic construct]

 Score =  138 bits (348), Expect = 3e-31,   Method: Compositional matrix adjust.
 Identities = 64/88 (72%), Positives = 73/88 (82%)

Query: 1  MSTPLPCNPKPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTGK 60
          MS  +P NPKPFLN LTGK V+ KLKWG EYKG LVS DGYMN QLA+TEE+I+G  TG 
Sbjct: 1  MSAGMPINPKPFLNGLTGKPVLVKLKWGQEYKGFLVSVDGYMNMQLANTEEVIEGSVTGN 60

Query: 61 LGEVLIRCNNILYIRGAEEGDEEGEMRE 88
          LGEVLIRCNN+LYI+G E+ DEEGEMR+
Sbjct: 61 LGEVLIRCNNVLYIKGMEDDDEEGEMRD 88

Source: Drosophila melanogaster

Species: Drosophila melanogaster

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|153792507|ref|NP_001093276.1| small nuclear ribonucleoprotein protein F [Bombyx mori] gi|95102986|gb|ABF51434.1| small nuclear ribonucleoprotein protein F [Bombyx mori]

 Score =  135 bits (340), Expect = 3e-30,   Method: Compositional matrix adjust.
 Identities = 60/78 (76%), Positives = 70/78 (89%)

Query: 1  MSTPLPCNPKPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTGK 60
          M+  +P NPKPFLN LTGKSV+ KLKWGHEYKG+LVSTDGYMN QLA+TEE++DG CTG 
Sbjct: 1  MAAAMPINPKPFLNSLTGKSVLVKLKWGHEYKGLLVSTDGYMNLQLANTEELVDGTCTGN 60

Query: 61 LGEVLIRCNNILYIRGAE 78
          LGEVLIRCNN+LY+RGA+
Sbjct: 61 LGEVLIRCNNVLYVRGAD 78

Source: Bombyx mori

Species: Bombyx mori

Genus: Bombyx

Family: Bombycidae

Order: Lepidoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|357605279|gb|EHJ64538.1| small nuclear ribonucleoprotein F [Danaus plexippus]

 Score =  133 bits (335), Expect = 1e-29,   Method: Compositional matrix adjust.
 Identities = 59/77 (76%), Positives = 68/77 (88%)

Query: 1  MSTPLPCNPKPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTGK 60
          M+  +P NPKPFLN LTGK+V+ KLKWGHEYKG+LVS DGYMN QLA+TEEI+DG CTG 
Sbjct: 1  MAASMPINPKPFLNSLTGKAVLVKLKWGHEYKGLLVSADGYMNLQLANTEEIVDGSCTGN 60

Query: 61 LGEVLIRCNNILYIRGA 77
          LGEVLIRCNN+LY+RGA
Sbjct: 61 LGEVLIRCNNVLYVRGA 77

Source: Danaus plexippus

Species: Danaus plexippus

Genus: Danaus

Family: Nymphalidae

Order: Lepidoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	88
FB|FBgn0000426	88	SmF "Small ribonucleoprotein p	0.852	0.852	0.733	2.5e-26
UNIPROTKB|F1P4B8	85	SNRPF "Uncharacterized protein	0.806	0.835	0.774	4.6e-25
UNIPROTKB|Q3T0Z8	86	SNRPF "Small nuclear ribonucle	0.806	0.825	0.774	4.6e-25
UNIPROTKB|F1Q0L5	111	SNRPF "Uncharacterized protein	0.806	0.639	0.774	4.6e-25
UNIPROTKB|P62306	86	SNRPF "Small nuclear ribonucle	0.806	0.825	0.774	4.6e-25
UNIPROTKB|F1SQR4	86	SNRPF "Uncharacterized protein	0.806	0.825	0.774	4.6e-25
MGI|MGI:1917128	86	Snrpf "small nuclear ribonucle	0.806	0.825	0.774	4.6e-25
RGD|1588229	86	Snrpf "small nuclear ribonucle	0.806	0.825	0.774	4.6e-25
ZFIN|ZDB-GENE-040930-9	86	snrpf "small nuclear ribonucle	0.806	0.825	0.760	7.6e-25
WB|WBGene00004918	85	snr-5 [Caenorhabditis elegans	0.840	0.870	0.689	9.7e-25

FB|FBgn0000426 SmF "Small ribonucleoprotein particle protein SmF" [Drosophila melanogaster (taxid:7227)]

 Score = 297 (109.6 bits), Expect = 2.5e-26, P = 2.5e-26
 Identities = 55/75 (73%), Positives = 62/75 (82%)

Query:     1 MSTPLPCNPKPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTGK 60
             MS  +P NPKPFLN LTGK V+ KLKWG EYKG LVS DGYMN QLA+TEE+I+G  TG 
Sbjct:     1 MSAGMPINPKPFLNGLTGKPVLVKLKWGQEYKGFLVSVDGYMNMQLANTEEVIEGSVTGN 60

Query:    61 LGEVLIRCNNILYIR 75
             LGEVLIRCNN+LYI+
Sbjct:    61 LGEVLIRCNNVLYIK 75

GO:0030532 "small nuclear ribonucleoprotein complex" evidence=ISS;NAS

GO:0000398 "mRNA splicing, via spliceosome" evidence=IC;ISS;NAS

GO:0005681 "spliceosomal complex" evidence=ISS;NAS

GO:0007052 "mitotic spindle organization" evidence=IMP

GO:0071011 "precatalytic spliceosome" evidence=IDA

GO:0071013 "catalytic step 2 spliceosome" evidence=IDA

UNIPROTKB|F1P4B8 SNRPF "Uncharacterized protein" [Gallus gallus (taxid:9031)]

 Score = 285 (105.4 bits), Expect = 4.6e-25, P = 4.6e-25
 Identities = 55/71 (77%), Positives = 59/71 (83%)

Query:     5 LPCNPKPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTGKLGEV 64
             LP NPKPFLN LTGK V+ KLKWG EYKG LVS DGYMN QLA+TEE IDG  +G LGEV
Sbjct:     2 LPLNPKPFLNGLTGKPVMVKLKWGMEYKGYLVSVDGYMNMQLANTEEYIDGALSGHLGEV 61

Query:    65 LIRCNNILYIR 75
             LIRCNN+LYIR
Sbjct:    62 LIRCNNVLYIR 72

GO:0003723 "RNA binding" evidence=IEA

GO:0005683 "U7 snRNP" evidence=IEA

GO:0005689 "U12-type spliceosomal complex" evidence=IEA

GO:0008380 "RNA splicing" evidence=IEA

GO:0071013 "catalytic step 2 spliceosome" evidence=IEA

UNIPROTKB|Q3T0Z8 SNRPF "Small nuclear ribonucleoprotein F" [Bos taurus (taxid:9913)]

 Score = 285 (105.4 bits), Expect = 4.6e-25, P = 4.6e-25
 Identities = 55/71 (77%), Positives = 59/71 (83%)

Query:     5 LPCNPKPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTGKLGEV 64
             LP NPKPFLN LTGK V+ KLKWG EYKG LVS DGYMN QLA+TEE IDG  +G LGEV
Sbjct:     3 LPLNPKPFLNGLTGKPVMVKLKWGMEYKGYLVSVDGYMNMQLANTEEYIDGALSGHLGEV 62

Query:    65 LIRCNNILYIR 75
             LIRCNN+LYIR
Sbjct:    63 LIRCNNVLYIR 73

GO:0005683 "U7 snRNP" evidence=ISS

GO:0071013 "catalytic step 2 spliceosome" evidence=IEA

GO:0008380 "RNA splicing" evidence=IEA

GO:0005689 "U12-type spliceosomal complex" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

GO:0006397 "mRNA processing" evidence=IEA

UNIPROTKB|F1Q0L5 SNRPF "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 285 (105.4 bits), Expect = 4.6e-25, P = 4.6e-25
 Identities = 55/71 (77%), Positives = 59/71 (83%)

Query:     5 LPCNPKPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTGKLGEV 64
             LP NPKPFLN LTGK V+ KLKWG EYKG LVS DGYMN QLA+TEE IDG  +G LGEV
Sbjct:    28 LPLNPKPFLNGLTGKPVMVKLKWGMEYKGYLVSVDGYMNMQLANTEEYIDGALSGHLGEV 87

Query:    65 LIRCNNILYIR 75
             LIRCNN+LYIR
Sbjct:    88 LIRCNNVLYIR 98

GO:0071013 "catalytic step 2 spliceosome" evidence=IEA

GO:0008380 "RNA splicing" evidence=IEA

GO:0005689 "U12-type spliceosomal complex" evidence=IEA

GO:0005683 "U7 snRNP" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

UNIPROTKB|P62306 SNRPF "Small nuclear ribonucleoprotein F" [Homo sapiens (taxid:9606)]

 Score = 285 (105.4 bits), Expect = 4.6e-25, P = 4.6e-25
 Identities = 55/71 (77%), Positives = 59/71 (83%)

Query:     5 LPCNPKPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTGKLGEV 64
             LP NPKPFLN LTGK V+ KLKWG EYKG LVS DGYMN QLA+TEE IDG  +G LGEV
Sbjct:     3 LPLNPKPFLNGLTGKPVMVKLKWGMEYKGYLVSVDGYMNMQLANTEEYIDGALSGHLGEV 62

Query:    65 LIRCNNILYIR 75
             LIRCNN+LYIR
Sbjct:    63 LIRCNNVLYIR 73

GO:0005681 "spliceosomal complex" evidence=IDA

GO:0008380 "RNA splicing" evidence=IMP;TAS

GO:0030532 "small nuclear ribonucleoprotein complex" evidence=IDA

GO:0003723 "RNA binding" evidence=IMP

GO:0071013 "catalytic step 2 spliceosome" evidence=IDA

GO:0005683 "U7 snRNP" evidence=IDA

GO:0005689 "U12-type spliceosomal complex" evidence=IDA

GO:0000398 "mRNA splicing, via spliceosome" evidence=IC;TAS

GO:0000387 "spliceosomal snRNP assembly" evidence=TAS

GO:0005654 "nucleoplasm" evidence=TAS

GO:0005829 "cytosol" evidence=TAS

GO:0006366 "transcription from RNA polymerase II promoter" evidence=TAS

GO:0006369 "termination of RNA polymerase II transcription" evidence=TAS

GO:0006397 "mRNA processing" evidence=TAS

GO:0008334 "histone mRNA metabolic process" evidence=TAS

GO:0010467 "gene expression" evidence=TAS

GO:0016070 "RNA metabolic process" evidence=TAS

GO:0034660 "ncRNA metabolic process" evidence=TAS

UNIPROTKB|F1SQR4 SNRPF "Uncharacterized protein" [Sus scrofa (taxid:9823)]

 Score = 285 (105.4 bits), Expect = 4.6e-25, P = 4.6e-25
 Identities = 55/71 (77%), Positives = 59/71 (83%)

Query:     5 LPCNPKPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTGKLGEV 64
             LP NPKPFLN LTGK V+ KLKWG EYKG LVS DGYMN QLA+TEE IDG  +G LGEV
Sbjct:     3 LPLNPKPFLNGLTGKPVMVKLKWGMEYKGYLVSVDGYMNMQLANTEEYIDGALSGHLGEV 62

Query:    65 LIRCNNILYIR 75
             LIRCNN+LYIR
Sbjct:    63 LIRCNNVLYIR 73

GO:0071013 "catalytic step 2 spliceosome" evidence=IEA

GO:0008380 "RNA splicing" evidence=IEA

GO:0005689 "U12-type spliceosomal complex" evidence=IEA

GO:0005683 "U7 snRNP" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

MGI|MGI:1917128 Snrpf "small nuclear ribonucleoprotein polypeptide F" [Mus musculus (taxid:10090)]

 Score = 285 (105.4 bits), Expect = 4.6e-25, P = 4.6e-25
 Identities = 55/71 (77%), Positives = 59/71 (83%)

Query:     5 LPCNPKPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTGKLGEV 64
             LP NPKPFLN LTGK V+ KLKWG EYKG LVS DGYMN QLA+TEE IDG  +G LGEV
Sbjct:     3 LPLNPKPFLNGLTGKPVMVKLKWGMEYKGYLVSVDGYMNMQLANTEEYIDGALSGHLGEV 62

Query:    65 LIRCNNILYIR 75
             LIRCNN+LYIR
Sbjct:    63 LIRCNNVLYIR 73

GO:0003723 "RNA binding" evidence=ISO

GO:0005634 "nucleus" evidence=IEA

GO:0005681 "spliceosomal complex" evidence=ISO

GO:0005683 "U7 snRNP" evidence=ISO

GO:0005689 "U12-type spliceosomal complex" evidence=ISO

GO:0006396 "RNA processing" evidence=IEA

GO:0006397 "mRNA processing" evidence=IEA

GO:0008380 "RNA splicing" evidence=ISO

GO:0030529 "ribonucleoprotein complex" evidence=IEA

GO:0030532 "small nuclear ribonucleoprotein complex" evidence=ISO

GO:0071013 "catalytic step 2 spliceosome" evidence=ISO

RGD|1588229 Snrpf "small nuclear ribonucleoprotein polypeptide F" [Rattus norvegicus (taxid:10116)]

 Score = 285 (105.4 bits), Expect = 4.6e-25, P = 4.6e-25
 Identities = 55/71 (77%), Positives = 59/71 (83%)

Query:     5 LPCNPKPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTGKLGEV 64
             LP NPKPFLN LTGK V+ KLKWG EYKG LVS DGYMN QLA+TEE IDG  +G LGEV
Sbjct:     3 LPLNPKPFLNGLTGKPVMVKLKWGMEYKGYLVSVDGYMNMQLANTEEYIDGALSGHLGEV 62

Query:    65 LIRCNNILYIR 75
             LIRCNN+LYIR
Sbjct:    63 LIRCNNVLYIR 73

GO:0003723 "RNA binding" evidence=IEA;ISO

GO:0005681 "spliceosomal complex" evidence=ISO

GO:0005683 "U7 snRNP" evidence=IEA;ISO

GO:0005689 "U12-type spliceosomal complex" evidence=IEA;ISO

GO:0008380 "RNA splicing" evidence=IEA;ISO

GO:0030532 "small nuclear ribonucleoprotein complex" evidence=ISO

GO:0071013 "catalytic step 2 spliceosome" evidence=IEA;ISO

ZFIN|ZDB-GENE-040930-9 snrpf "small nuclear ribonucleoprotein polypeptide F" [Danio rerio (taxid:7955)]

 Score = 283 (104.7 bits), Expect = 7.6e-25, P = 7.6e-25
 Identities = 54/71 (76%), Positives = 58/71 (81%)

Query:     5 LPCNPKPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTGKLGEV 64
             LP NPKPFLN LTGK V+ KLKWG EYKG LVS DGYMN QLA+TEE +DG   G LGEV
Sbjct:     3 LPLNPKPFLNGLTGKPVMVKLKWGMEYKGYLVSVDGYMNMQLANTEEYVDGALAGHLGEV 62

Query:    65 LIRCNNILYIR 75
             LIRCNN+LYIR
Sbjct:    63 LIRCNNVLYIR 73

GO:0005634 "nucleus" evidence=IEA

GO:0006396 "RNA processing" evidence=IEA

GO:0030529 "ribonucleoprotein complex" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

WB|WBGene00004918 snr-5 [Caenorhabditis elegans (taxid:6239)]

 Score = 282 (104.3 bits), Expect = 9.7e-25, P = 9.7e-25
 Identities = 51/74 (68%), Positives = 58/74 (78%)

Query:     1 MSTPLPCNPKPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTGK 60
             MS   P NPKPFLN LTGK V+CKLKWG EYKG+LV+ D YMN QLA  EE IDG+  G 
Sbjct:     1 MSAVQPVNPKPFLNSLTGKFVVCKLKWGMEYKGVLVAVDSYMNLQLAHAEEYIDGNSQGN 60

Query:    61 LGEVLIRCNNILYI 74
             LGE+LIRCNN+LY+
Sbjct:    61 LGEILIRCNNVLYV 74

GO:0005634 "nucleus" evidence=IEA

GO:0006396 "RNA processing" evidence=IEA

GO:0009792 "embryo development ending in birth or egg hatching" evidence=IMP

GO:0000003 "reproduction" evidence=IMP

GO:0002119 "nematode larval development" evidence=IMP

GO:0040007 "growth" evidence=IMP

GO:0040039 "inductive cell migration" evidence=IMP

GO:0018996 "molting cycle, collagen and cuticulin-based cuticle" evidence=IMP

GO:0006898 "receptor-mediated endocytosis" evidence=IMP

GO:0032940 "secretion by cell" evidence=IMP

GO:0040027 "negative regulation of vulval development" evidence=IMP

GO:0006915 "apoptotic process" evidence=IMP

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

ID	Name	Annotated EC number	Identity	Query coverage	Hit coverage	RBH(Q2H)	RBH(H2Q)
Q3T0Z8	RUXF_BOVIN	No assigned EC number	0.7671	0.8295	0.8488	yes	N/A
Q24297	RUXF_DROME	No assigned EC number	0.7272	1.0	1.0	yes	N/A
B6YUU5	RUXX_THEON	No assigned EC number	0.3906	0.7272	0.8205	yes	N/A
C5A1H1	RUXX_THEGJ	No assigned EC number	0.3571	0.6363	0.7368	yes	N/A
P62321	RUXF_XENLA	No assigned EC number	0.7671	0.8295	0.8488	N/A	N/A
P34659	RUXF_CAEEL	No assigned EC number	0.6463	0.9318	0.9647	yes	N/A
Q465S1	RUXX_METBF	No assigned EC number	0.3636	0.75	0.9166	yes	N/A
Q9SUM2	RUXF_ARATH	No assigned EC number	0.6923	0.8863	0.8863	yes	N/A
P57670	RUXX_THEAC	No assigned EC number	0.3472	0.8181	0.8674	yes	N/A
P62307	RUXF_MOUSE	No assigned EC number	0.7671	0.8295	0.8488	yes	N/A
P62306	RUXF_HUMAN	No assigned EC number	0.7671	0.8295	0.8488	yes	N/A
O26745	RUXX_METTH	No assigned EC number	0.5185	0.6136	0.6666	yes	N/A
O29386	RUXX_ARCFU	No assigned EC number	0.3506	0.875	1.0	yes	N/A
Q54XP2	RUXF_DICDI	No assigned EC number	0.5875	0.8977	0.8681	yes	N/A
Q97BU5	RUXX_THEVO	No assigned EC number	0.3417	0.8636	0.9156	yes	N/A
Q12U30	RUXX_METBU	No assigned EC number	0.3939	0.75	0.9166	yes	N/A
Q8TL47	RUXX_METAC	No assigned EC number	0.3636	0.75	0.9166	yes	N/A
Q8U0P4	RUXX_PYRFU	No assigned EC number	0.4032	0.7045	0.8157	yes	N/A
P54999	RUXF_YEAST	No assigned EC number	0.5394	0.8522	0.8720	yes	N/A
Q9V0Y8	RUXX_PYRAB	No assigned EC number	0.3934	0.6931	0.8133	yes	N/A
Q0W8R9	RUXX_UNCMA	No assigned EC number	0.3333	0.75	0.9166	yes	N/A
Q5JIE0	RUXX_PYRKO	No assigned EC number	0.3833	0.6818	0.7894	yes	N/A
Q9P5Z8	RUXF_NEUCR	No assigned EC number	0.5238	0.9431	0.9222	N/A	N/A
O59734	RUXF_SCHPO	No assigned EC number	0.6142	0.7954	0.8974	yes	N/A
O74016	RUXX_PYRHO	No assigned EC number	0.3934	0.6931	0.8133	yes	N/A
Q8PZZ9	RUXX_METMA	No assigned EC number	0.3484	0.75	0.9166	yes	N/A

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database

ID	Length	Definition	E-value
Query	88
cd01722	69	cd01722, Sm_F, Sm protein F	2e-44
cd01726	68	cd01726, LSm6, Like-Sm protein 6	6e-24
pfam01423	66	pfam01423, LSM, LSM domain	8e-21
smart00651	67	smart00651, Sm, snRNP Sm proteins	2e-20
COG1958	79	COG1958, LSM1, Small nuclear ribonucleoprotein (sn	2e-17
PRK00737	72	PRK00737, PRK00737, small nuclear ribonucleoprotei	7e-16
cd01731	69	cd01731, archaeal_Sm1, archaeal Sm protein 1	5e-15
cd00600	63	cd00600, Sm_like, Sm and related proteins	3e-14
cd11678	69	cd11678, archaeal_LSm, archaeal Like-Sm protein	3e-06
cd01723	76	cd01723, LSm4, Like-Sm protein 4	1e-05
cd01733	78	cd01733, LSm10, Like-Sm protein 10	3e-04

>gnl|CDD|212469 cd01722, Sm_F, Sm protein F

 Score =  137 bits (347), Expect = 2e-44
 Identities = 54/69 (78%), Positives = 56/69 (81%)

Query: 8  NPKPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTGKLGEVLIR 67
          NPKPFLN LTGK VI KLKWG EYKG LVS D YMN QLA+TEE IDG  TG LGEVLIR
Sbjct: 1  NPKPFLNGLTGKPVIVKLKWGMEYKGTLVSVDSYMNLQLANTEEYIDGKFTGNLGEVLIR 60

Query: 68 CNNILYIRG 76
          CNN+LYIR 
Sbjct: 61 CNNVLYIRE 69

The eukaryotic Sm proteins (B/B', D1, D2, D3, E, F and G) assemble into a hetero-heptameric ring around the Sm site of the 2,2,7-trimethyl guanosine (m3G) capped U1, U2, U4 and U5 snRNAs (Sm snRNAs) forming the core of the snRNP particle. The snRNP particle, in turn, assembles with other components onto the pre-mRNA to form the spliceosome which is responsible for the excision of introns and the ligation of exons. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Sm subunit F is capable of forming both homo- and hetero-heptamer ring structures. To form the hetero-heptamer, Sm subunit F initially binds subunits E and G to form a trimer which then assembles onto snRNA along with the D3/B and D1/D2 heterodimers. Length = 69

>gnl|CDD|212473 cd01726, LSm6, Like-Sm protein 6

 Score = 85.3 bits (212), Expect = 6e-24
 Identities = 34/68 (50%), Positives = 41/68 (60%)

Query: 8  NPKPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTGKLGEVLIR 67
           P  FL  + GK V+ KLK G EY+G+L   DGYMN  L  TEE +DG    K G+  IR
Sbjct: 1  TPSKFLKKIIGKPVVVKLKNGVEYRGVLACLDGYMNLVLEDTEEYVDGQLVAKYGDAFIR 60

Query: 68 CNNILYIR 75
           NN+LYI 
Sbjct: 61 GNNVLYIS 68

The eukaryotic LSm proteins (LSm2-8 or LSm1-7) assemble into a hetero-heptameric ring around the 3'-terminus uridylation tag of the gamma-methyl triphosphate (gamma-m-P3) capped U6 snRNA. LSm2-8 form the core of the snRNP particle that, in turn, assembles with other components onto the pre-mRNA to form the spliceosome which is responsible for the excision of introns and the ligation of exons. LSm1-7 is involved in recognition of the 3' uridylation tag and recruitment of the decapping machinery. LSm657 is believed to be an assembly intermediate for both the LSm1-7 and LSm2-8 rings. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Length = 68

>gnl|CDD|201787 pfam01423, LSM, LSM domain

 Score = 77.6 bits (192), Expect = 8e-21
 Identities = 30/64 (46%), Positives = 34/64 (53%)

Query: 11 PFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTGKLGEVLIRCNN 70
           FL  L GK V  +LK G E +G L   D +MN  L   EE I      KLG VLIR NN
Sbjct: 1  KFLQKLLGKRVTVELKNGRELRGTLKGFDQFMNLVLDDVEETIKDGKVNKLGLVLIRGNN 60

Query: 71 ILYI 74
          I+ I
Sbjct: 61 IVLI 64

The LSM domain contains Sm proteins as well as other related LSM (Like Sm) proteins. The U1, U2, U4/U6, and U5 small nuclear ribonucleoprotein particles (snRNPs) involved in pre-mRNA splicing contain seven Sm proteins (B/B', D1, D2, D3, E, F and G) in common, which assemble around the Sm site present in four of the major spliceosomal small nuclear RNAs. The U6 snRNP binds to the LSM (Like Sm) proteins. Sm proteins are also found in archaebacteria, which do not have any splicing apparatus suggesting a more general role for Sm proteins. All Sm proteins contain a common sequence motif in two segments, Sm1 and Sm2, separated by a short variable linker. This family also includes the bacterial Hfq (host factor Q) proteins. Hfq are also RNA-binding proteins, that form hexameric rings. Length = 66

>gnl|CDD|197820 smart00651, Sm, snRNP Sm proteins

 Score = 76.4 bits (189), Expect = 2e-20
 Identities = 32/66 (48%), Positives = 38/66 (57%), Gaps = 1/66 (1%)

Query: 11 PFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEII-DGHCTGKLGEVLIRCN 69
           FL  L GK V+ +LK G EY+G L   D +MN  L   EE + DG    KLG V IR N
Sbjct: 1  KFLKKLIGKRVLVELKNGREYRGTLKGFDQFMNLVLEDVEETVKDGEKKRKLGLVFIRGN 60

Query: 70 NILYIR 75
          NI+YI 
Sbjct: 61 NIVYII 66

small nuclear ribonucleoprotein particles (snRNPs) involved in pre-mRNA splicing. Length = 67

>gnl|CDD|224869 COG1958, LSM1, Small nuclear ribonucleoprotein (snRNP) homolog [Transcription]

 Score = 69.6 bits (171), Expect = 2e-17
 Identities = 34/76 (44%), Positives = 40/76 (52%), Gaps = 4/76 (5%)

Query: 3  TPLPCNPKPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDG----HCT 58
          + L   P  FL  L  K V+ KLK G EY+G LV  D YMN  L   EEII      +  
Sbjct: 2  SMLGPLPLSFLKKLLNKRVLVKLKNGREYRGTLVGFDQYMNLVLDDVEEIISHDGEKNVR 61

Query: 59 GKLGEVLIRCNNILYI 74
             GEVLIR +NI+ I
Sbjct: 62 RLGGEVLIRGDNIVLI 77

Length = 79

>gnl|CDD|179104 PRK00737, PRK00737, small nuclear ribonucleoprotein; Provisional

 Score = 65.0 bits (159), Expect = 7e-16
 Identities = 24/56 (42%), Positives = 36/56 (64%)

Query: 19 KSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTGKLGEVLIRCNNILYI 74
            V+ +LK G E++G L   D +MN  L + EEI DG    KLG+V+IR +N++Y+
Sbjct: 15 SPVLVRLKGGREFRGELQGYDIHMNLVLDNAEEIQDGEVVRKLGKVVIRGDNVVYV 70

Length = 72

>gnl|CDD|212478 cd01731, archaeal_Sm1, archaeal Sm protein 1

 Score = 62.6 bits (153), Expect = 5e-15
 Identities = 25/57 (43%), Positives = 38/57 (66%)

Query: 18 GKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTGKLGEVLIRCNNILYI 74
           K+V+ KLK G E +G+L   D ++N  L + EEII+G    KLG VL+R +N+++I
Sbjct: 11 NKNVLVKLKGGKEVRGVLKGFDQHLNLVLENAEEIIEGESVRKLGTVLVRGDNVVFI 67

The archaeal Sm1 proteins: The Sm proteins are conserved in all three domains of life and are always associated with U-rich RNA sequences. They function to mediate RNA-RNA interactions and RNA biogenesis. All Sm proteins contain a common sequence motif in two segments, Sm1 and Sm2, separated by a short variable linker. Eukaryotic Sm proteins form part of specific small nuclear ribonucleoproteins (snRNPs) that are involved in the processing of pre-mRNAs to mature mRNAs, and are a major component of the eukaryotic spliceosome. Most snRNPs consist of seven Sm proteins (B/B', D1, D2, D3, E, F and G) arranged in a ring on a uridine-rich sequence (Sm site), plus a small nuclear RNA (snRNA) (either U1, U2, U5 or U4/6). Since archaebacteria do not have any splicing apparatus, their Sm proteins may play a more general role. Archaeal LSm proteins are likely to represent the ancestral Sm domain. Length = 69

>gnl|CDD|212462 cd00600, Sm_like, Sm and related proteins

 Score = 60.7 bits (148), Expect = 3e-14
 Identities = 26/63 (41%), Positives = 31/63 (49%)

Query: 13 LNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTGKLGEVLIRCNNIL 72
          L    GK+V  +LK G    G LV+ D YMN  L    E         LG VLIR +NI+
Sbjct: 1  LKDFIGKTVSVELKDGRVLTGTLVAFDKYMNLVLDDVVETGRDGKVRVLGLVLIRGSNIV 60

Query: 73 YIR 75
           IR
Sbjct: 61 SIR 63

The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes. Length = 63

>gnl|CDD|212489 cd11678, archaeal_LSm, archaeal Like-Sm protein

 Score = 40.6 bits (95), Expect = 3e-06
 Identities = 22/60 (36%), Positives = 32/60 (53%), Gaps = 1/60 (1%)

Query: 16 LTGKSVICKLKW-GHEYKGILVSTDGYMNCQLASTEEIIDGHCTGKLGEVLIRCNNILYI 74
          L G  +  ++K   ++ +G LV+ D YMN  L  T E +       LG V++R NNIL I
Sbjct: 8  LVGSRIRVEMKGDENQLQGRLVAVDDYMNLHLTDTMECVGEEKVRSLGTVVLRGNNILLI 67

The archaeal Sm-like (LSm): The Sm proteins are conserved in all three domains of life and are always associated with U-rich RNA sequences. They function to mediate RNA-RNA interactions and RNA biogenesis. All Sm proteins contain a common sequence motif in two segments, Sm1 and Sm2, separated by a short variable linker. Eukaryotic Sm proteins form part of specific small nuclear ribonucleoproteins (snRNPs) that are involved in the processing of pre-mRNAs to mature mRNAs, and are a major component of the eukaryotic spliceosome. Most snRNPs consist of seven Sm proteins (B/B', D1, D2, D3, E, F and G) arranged in a ring on a uridine-rich sequence (Sm site), plus a small nuclear RNA (snRNA) (either U1, U2, U5 or U4/6). Since archaebacteria do not have any splicing apparatus, their Sm proteins may play a more general role. Archaeal LSm proteins are likely to represent the ancestral Sm domain. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes. Length = 69

>gnl|CDD|212470 cd01723, LSm4, Like-Sm protein 4

 Score = 39.5 bits (93), Expect = 1e-05
 Identities = 27/71 (38%), Positives = 36/71 (50%), Gaps = 4/71 (5%)

Query: 13 LNLLT---GKSVICKLKWGHEYKGILVSTDGYMNCQLAS-TEEIIDGHCTGKLGEVLIRC 68
          L+LL    G  V+ +LK G  Y G LV+ D +MN  L +      DG    K+ E  IR 
Sbjct: 3  LSLLRTAQGHPVLVELKNGETYNGHLVNCDNWMNIHLKNVICTSKDGDRFWKMPECYIRG 62

Query: 69 NNILYIRGAEE 79
          N I Y+R  +E
Sbjct: 63 NTIKYLRLPDE 73

The eukaryotic LSm proteins (LSm2-8 or LSm1-7) assemble into a hetero-heptameric ring around the 3'-terminus uridylation tag of the gamma-methyl triphosphate (gamma-m-P3) capped U6 snRNA. LSm2-8 form the core of the snRNP particle that, in turn, assembles with other components onto the pre-mRNA to form the spliceosome which is responsible for the excision of introns and the ligation of exons. LSm1-7 is involved in recognition of the 3' uridylation tag and recruitment of the decapping machinery. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Length = 76

>gnl|CDD|212480 cd01733, LSm10, Like-Sm protein 10

 Score = 35.6 bits (83), Expect = 3e-04
 Identities = 17/64 (26%), Positives = 29/64 (45%), Gaps = 2/64 (3%)

Query: 12 FLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLA-STEEIIDGHCTGKLGEVLIRCNN 70
           L  L G+    +L+     +GI+ + DG+MN  L+ +T     G       E  ++  N
Sbjct: 13 LLQALQGRVTTVELRNETSVRGIIDNVDGFMNITLSDATFTDRRGKQH-HFDEFFVQGRN 71

Query: 71 ILYI 74
          I Y+
Sbjct: 72 IRYV 75

The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. LSm10 is an SmD1-like protein which is thought to bind U7 snRNA along with LSm11 and five other Sm subunits to form a 7-membered ring structure. LSm10 and the U7 snRNP of which it is a part are thought to play an important role in histone mRNA 3' processing. Length = 78

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	88
cd01721	70	Sm_D3 The eukaryotic Sm and Sm-like (LSm) proteins	99.94
PRK00737	72	small nuclear ribonucleoprotein; Provisional	99.93
cd01726	67	LSm6 The eukaryotic Sm and Sm-like (LSm) proteins	99.93
cd01731	68	archaeal_Sm1 The archaeal sm1 proteins: The Sm pro	99.92
cd01722	68	Sm_F The eukaryotic Sm and Sm-like (LSm) proteins	99.92
cd01723	76	LSm4 The eukaryotic Sm and Sm-like (LSm) proteins	99.92
cd01724	90	Sm_D1 The eukaryotic Sm and Sm-like (LSm) proteins	99.92
cd01733	78	LSm10 The eukaryotic Sm and Sm-like (LSm) proteins	99.91
cd01719	72	Sm_G The eukaryotic Sm and Sm-like (LSm) proteins	99.91
cd01732	76	LSm5 The eukaryotic Sm and Sm-like (LSm) proteins	99.9
cd01725	81	LSm2 The eukaryotic Sm and Sm-like (LSm) proteins	99.9
cd01730	82	LSm3 The eukaryotic Sm and Sm-like (LSm) proteins	99.89
KOG3482|consensus	79		99.89
COG1958	79	LSM1 Small nuclear ribonucleoprotein (snRNP) homol	99.89
PF01423	67	LSM: LSM domain ; InterPro: IPR001163 This family	99.89
smart00651	67	Sm snRNP Sm proteins. small nuclear ribonucleoprot	99.88
cd01720	87	Sm_D2 The eukaryotic Sm and Sm-like (LSm) proteins	99.88
cd01729	81	LSm7 The eukaryotic Sm and Sm-like (LSm) proteins	99.87
cd00600	63	Sm_like The eukaryotic Sm and Sm-like (LSm) protei	99.85
cd01718	79	Sm_E The eukaryotic Sm and Sm-like (LSm) proteins	99.85
cd01717	79	Sm_B The eukaryotic Sm and Sm-like (LSm) proteins	99.85
cd01727	74	LSm8 The eukaryotic Sm and Sm-like (LSm) proteins	99.85
cd01728	74	LSm1 The eukaryotic Sm and Sm-like (LSm) proteins	99.84
KOG1783|consensus	77		99.82
cd06168	75	LSm9 The eukaryotic Sm and Sm-like (LSm) proteins	99.81
PTZ00138	89	small nuclear ribonucleoprotein; Provisional	99.78
KOG1780|consensus	77		99.76
KOG3293|consensus	134		99.73
KOG3460|consensus	91		99.7
KOG3448|consensus	96		99.68
KOG3172|consensus	119		99.66
KOG1775|consensus	84		99.63
KOG3428|consensus	109		99.57
KOG1781|consensus	108		99.52
KOG1784|consensus	96		99.34
KOG1774|consensus	88		99.3
KOG1782|consensus	129		99.28
KOG3168|consensus	177		99.26
KOG3459|consensus	114		98.76
PF14438	77	SM-ATX: Ataxin 2 SM domain; PDB: 1M5Q_1.	98.31
cd01739	66	LSm11_C The eukaryotic Sm and Sm-like (LSm) protei	98.18
PF12701	96	LSM14: Scd6-like Sm domain; PDB: 2RM4_A 2FB7_A 2VC	97.61
PF02237	48	BPL_C: Biotin protein ligase C terminal domain; In	97.05
PF06372	166	Gemin6: Gemin6 protein; InterPro: IPR009422 This f	96.89
cd01736	74	LSm14_N LSm14 (also known as RAP55) belongs to a f	96.81
PF11095	80	Gemin7: Gem-associated protein 7 (Gemin7); InterPr	96.72
PF10842	66	DUF2642: Protein of unknown function (DUF2642); In	96.51
cd01716	61	Hfq Hfq, an abundant, ubiquitous RNA-binding prote	96.3
cd01735	61	LSm12_N LSm12 belongs to a family of Sm-like prote	96.17
PRK14638	150	hypothetical protein; Provisional	96.16
TIGR02383	61	Hfq RNA chaperone Hfq. This model represents the R	95.86
PRK14639	140	hypothetical protein; Provisional	95.82
COG1923	77	Hfq Uncharacterized host factor I protein [General	95.74
PRK02001	152	hypothetical protein; Validated	95.62
PRK00395	79	hfq RNA-binding protein Hfq; Provisional	95.53
PRK14644	136	hypothetical protein; Provisional	95.25
PRK14640	152	hypothetical protein; Provisional	94.52
COG0779	153	Uncharacterized protein conserved in bacteria [Fun	94.5
cd01734	83	YlxS_C YxlS is a Bacillus subtilis gene of unknown	94.49
PRK14091	165	RNA-binding protein Hfq; Provisional	94.49
PF02576	141	DUF150: Uncharacterised BCR, YhbC family COG0779;	94.23
PRK14633	150	hypothetical protein; Provisional	94.16
PRK14645	154	hypothetical protein; Provisional	94.07
PRK14642	197	hypothetical protein; Provisional	93.65
PRK14643	164	hypothetical protein; Provisional	93.56
PRK14632	172	hypothetical protein; Provisional	93.53
PRK14636	176	hypothetical protein; Provisional	93.4
PRK14091	165	RNA-binding protein Hfq; Provisional	93.35
PRK14634	155	hypothetical protein; Provisional	93.32
PRK00092	154	ribosome maturation protein RimP; Reviewed	93.17
PRK14646	155	hypothetical protein; Provisional	93.04
PRK14647	159	hypothetical protein; Provisional	92.92
PRK14637	151	hypothetical protein; Provisional	92.14
PRK14631	174	hypothetical protein; Provisional	92.12
PRK06955	300	biotin--protein ligase; Provisional	91.29
PRK14641	173	hypothetical protein; Provisional	91.21
KOG1073|consensus	361		91.06
PRK11886	319	bifunctional biotin--[acetyl-CoA-carboxylase] synt	88.84
PRK14630	143	hypothetical protein; Provisional	87.59
TIGR00121	237	birA_ligase birA, biotin-[acetyl-CoA-carboxylase]	87.52
PRK14635	162	hypothetical protein; Provisional	87.37
PRK13325	592	bifunctional biotin--[acetyl-CoA-carboxylase] liga	86.17
PF03614	165	Flag1_repress: Repressor of phase-1 flagellin; Int	83.28
PRK09618	142	flgD flagellar basal body rod modification protein	81.76
COG0340	238	BirA Biotin-(acetyl-CoA carboxylase) ligase [Coenz	81.3
PF11607	101	DUF3247: Protein of unknown function (DUF3247); In	80.18

>cd01721 Sm_D3 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation

Probab=99.94  E-value=6.7e-26  Score=136.07  Aligned_cols=70  Identities=29%  Similarity=0.441  Sum_probs=65.1

Q ss_pred             cHHHHhhcCCCEEEEEEcCccEEEEEEEEecCCcceEEcceEEEecCeeeeeeceEEEeCCcEEEEEcCC
Q psy6372           9 PKPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTGKLGEVLIRCNNILYIRGAE   78 (88)
Q Consensus         9 p~~~L~~~i~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~d~~e~~~~~~~~~~~~v~IrG~~I~~I~~~d   78 (88)
                      |+.+|+++.|++|+|+|+||.+|+|+|.+||+|||++|+||.+...+++..+++.+||||++|+||++||
T Consensus         1 P~~~L~~~~g~~V~VeLk~g~~~~G~L~~~D~~MNl~L~~~~~~~~~g~~~~~~~v~IRG~nI~~v~lPd   70 (70)
T cd01721           1 PIKLLHEAEGHIVTVELKTGEVYRGKLIEAEDNMNCQLKDVTVTARDGRVSQLEQVYIRGSKIRFFILPD   70 (70)
T ss_pred             ChHHHhhCCCCEEEEEECCCcEEEEEEEEEcCCceeEEEEEEEECCCCcEeEcCcEEEeCCEEEEEEeCC
Confidence            7899999999999999999999999999999999999999998744445678999999999999999997

Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Sm subunit D3 heterodimerizes with subunit B and three such heterodimers form a hexameric ring structure with alternating B and D3 subunits. The D3 - B heterodimer also assembles into a heptameric ring containing D1, D2, E, F, and G subunits. Sm-like proteins exist in archaea as well as prokaryotes which form heptameric and hexameric ring structures similar to those found in eukaryotes.

>PRK00737 small nuclear ribonucleoprotein; Provisional

Probab=99.93  E-value=2.4e-25  Score=134.25  Aligned_cols=70  Identities=39%  Similarity=0.557  Sum_probs=66.0

Q ss_pred             CCcHHHHhhcCCCEEEEEEcCccEEEEEEEEecCCcceEEcceEEEecCeeeeeeceEEEeCCcEEEEEc
Q psy6372           7 CNPKPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTGKLGEVLIRCNNILYIRG   76 (88)
Q Consensus         7 ~~p~~~L~~~i~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~d~~e~~~~~~~~~~~~v~IrG~~I~~I~~   76 (88)
                      ..|+.+|++++|++|+|+|+||+.|+|+|.+||+|||++|+||.+..+++..++++.++|||++|++|.+
T Consensus         3 ~~P~~~L~~~~~k~V~V~lk~g~~~~G~L~~~D~~mNlvL~d~~e~~~~~~~~~lg~v~iRG~~V~~i~~   72 (72)
T PRK00737          3 QRPLDVLNNALNSPVLVRLKGGREFRGELQGYDIHMNLVLDNAEEIQDGEVVRKLGKVVIRGDNVVYVSP   72 (72)
T ss_pred             cchHHHHHHhCCCEEEEEECCCCEEEEEEEEEcccceeEEeeEEEEcCCCeEeEcCcEEEeCCEEEEEcC
Confidence            5899999999999999999999999999999999999999999998777677899999999999999963

>cd01726 LSm6 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation

Probab=99.93  E-value=2e-25  Score=132.85  Aligned_cols=67  Identities=46%  Similarity=0.850  Sum_probs=63.8

Q ss_pred             cHHHHhhcCCCEEEEEEcCccEEEEEEEEecCCcceEEcceEEEecCeeeeeeceEEEeCCcEEEEE
Q psy6372           9 PKPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTGKLGEVLIRCNNILYIR   75 (88)
Q Consensus         9 p~~~L~~~i~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~d~~e~~~~~~~~~~~~v~IrG~~I~~I~   75 (88)
                      |++||++++|++|+|+|+||++|+|+|.+||+|||++|+||.+..+++.+..++.++|||++|+||.
T Consensus         1 p~~~L~~~~~~~V~V~Lk~g~~~~G~L~~~D~~mNlvL~~~~~~~~~~~~~~~~~v~IRG~~I~~I~   67 (67)
T cd01726           1 PSEFLKAIIGRPVVVKLNSGVDYRGILACLDGYMNIALEQTEEYVNGQLKNKYGDAFIRGNNVLYIS   67 (67)
T ss_pred             CHHHHHhhCCCeEEEEECCCCEEEEEEEEEccceeeEEeeEEEEeCCceeeEeCCEEEECCEEEEEC
Confidence            8999999999999999999999999999999999999999999877777889999999999999984

Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. LSm6 is one of at least seven subunits that assemble onto U6 snRNA to form a seven-membered ring structure. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes.

>cd01731 archaeal_Sm1 The archaeal sm1 proteins: The Sm proteins are conserved in all three domains of life and are always associated with U-rich RNA sequences

Probab=99.92  E-value=9.8e-25  Score=130.01  Aligned_cols=68  Identities=43%  Similarity=0.527  Sum_probs=64.3

Q ss_pred             cHHHHhhcCCCEEEEEEcCccEEEEEEEEecCCcceEEcceEEEecCeeeeeeceEEEeCCcEEEEEc
Q psy6372           9 PKPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTGKLGEVLIRCNNILYIRG   76 (88)
Q Consensus         9 p~~~L~~~i~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~d~~e~~~~~~~~~~~~v~IrG~~I~~I~~   76 (88)
                      |+++|++++|++|+|+|++|+.|.|+|.+||+|||++|+||.+...+...+.++.++|||++|++|.+
T Consensus         1 p~~~L~~~~~~~V~V~l~~g~~~~G~L~~~D~~mNlvL~~~~e~~~~~~~~~lg~~~iRG~~I~~i~~   68 (68)
T cd01731           1 PLDVLKDSLNKPVLVKLKGGKEVRGRLKSYDQHMNLVLEDAEEIDDGEPVRKYGRVVIRGDNVLFISP   68 (68)
T ss_pred             ChHHHHHhcCCEEEEEECCCCEEEEEEEEECCcceEEEeeEEEEecCCeEeEcCcEEEeCCEEEEEcC
Confidence            88999999999999999999999999999999999999999998766678899999999999999974

They function to mediate RNA-RNA interactions and RNA biogenesis. All Sm proteins contain a common sequence motif in two segments, Sm1 and Sm2, separated by a short variable linker. Eukaryotic Sm proteins form part of specific small nuclear ribonucleoproteins (snRNPs) that are involved in the processing of pre-mRNAs to mature mRNAs, and are a major component of the eukaryotic spliceosome. Most snRNPs consist of seven Sm proteins (B/B', D1, D2, D3, E, F and G) arranged in a ring on a uridine-rich sequence (Sm site), plus a small nuclear RNA (snRNA) (either U1, U2, U5 or U4/6). Since archaebacteria do not have any splicing apparatus, Sm proteins of archaebacteria may play a more general role. Archaeal Lsm proteins are likely to represent the ancestral Sm domain.

>cd01722 Sm_F The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation

Probab=99.92  E-value=7.6e-25  Score=130.71  Aligned_cols=68  Identities=79%  Similarity=1.246  Sum_probs=64.0

Q ss_pred             CcHHHHhhcCCCEEEEEEcCccEEEEEEEEecCCcceEEcceEEEecCeeeeeeceEEEeCCcEEEEE
Q psy6372           8 NPKPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTGKLGEVLIRCNNILYIR   75 (88)
Q Consensus         8 ~p~~~L~~~i~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~d~~e~~~~~~~~~~~~v~IrG~~I~~I~   75 (88)
                      .|+++|++++|++|+|+|+||++|+|+|.+||+|||++|+||.+..++.....+|.++|||++|+||.
T Consensus         1 ~p~~~L~~~~g~~V~V~Lk~g~~~~G~L~~~D~~mNi~L~~~~e~~~~~~~~~lg~~~IRG~~I~~i~   68 (68)
T cd01722           1 NPKPFLNDLTGKPVIVKLKWGMEYKGTLVSVDSYMNLQLANTEEYIDGKSTGNLGEVLIRCNNVLYIR   68 (68)
T ss_pred             CHHHHHHHcCCCEEEEEECCCcEEEEEEEEECCCEEEEEeeEEEEeCCccccCcCcEEEECCEEEEEC
Confidence            58999999999999999999999999999999999999999999877766789999999999999983

Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Sm subunit F is capable of forming both homo- and hetero-heptamer ring structures. To form the hetero-heptamer, Sm subunit F initially binds subunits E and G to form a trimer which then assembles onto snRNA along with the D3/B and D1/D2 heterodimers.

>cd01723 LSm4 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation

Probab=99.92  E-value=9.3e-25  Score=132.86  Aligned_cols=73  Identities=33%  Similarity=0.440  Sum_probs=66.6

Q ss_pred             CcHHHHhhcCCCEEEEEEcCccEEEEEEEEecCCcceEEcceEEEe-cCeeeeeeceEEEeCCcEEEEEcCCCC
Q psy6372           8 NPKPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEII-DGHCTGKLGEVLIRCNNILYIRGAEEG   80 (88)
Q Consensus         8 ~p~~~L~~~i~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~d~~e~~-~~~~~~~~~~v~IrG~~I~~I~~~d~~   80 (88)
                      .|++||+++.|++|.|+|+||++|+|+|.+||+|||++|+||++.. +|+....++.+||||++|+||++||+.
T Consensus         1 ~Pl~~L~~~~g~~V~VeLkng~~~~G~L~~~D~~mNi~L~~~~~~~~~g~~~~~~~~v~IRG~~I~~i~~p~~~   74 (76)
T cd01723           1 LPLSLLKTAQNHPMLVELKNGETYNGHLVNCDNWMNIHLREVICTSKDGDKFWKMPECYIRGNTIKYLRVPDEI   74 (76)
T ss_pred             CchHHHHhcCCCEEEEEECCCCEEEEEEEEEcCCCceEEEeEEEECCCCcEeeeCCcEEEeCCEEEEEEcCHHH
Confidence            3899999999999999999999999999999999999999999873 454556789999999999999999864

Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. LSm4 is one of at least seven subunits that assemble onto U6 snRNA to form a seven-membered ring structure. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes.

>cd01724 Sm_D1 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation

Probab=99.92  E-value=1.6e-24  Score=135.83  Aligned_cols=73  Identities=29%  Similarity=0.322  Sum_probs=68.6

Q ss_pred             cHHHHhhcCCCEEEEEEcCccEEEEEEEEecCCcceEEcceEEEecCeeeeeeceEEEeCCcEEEEEcCCCCC
Q psy6372           9 PKPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTGKLGEVLIRCNNILYIRGAEEGD   81 (88)
Q Consensus         9 p~~~L~~~i~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~d~~e~~~~~~~~~~~~v~IrG~~I~~I~~~d~~~   81 (88)
                      ++.||+++.|++|+|+|+||.+|+|+|.++|+|||++|+||+++.+++....++.++|||++|+||++||+.+
T Consensus         2 ~~~fL~~l~g~~V~VeLKng~~~~G~L~~vD~~MNl~L~~a~~~~~~~~~~~~~~v~IRG~nI~yi~lPd~l~   74 (90)
T cd01724           2 LVRFLMKLTNETVTIELKNGTIVHGTITGVDPSMNTHLKNVKLTLKGRNPVPLDTLSIRGNNIRYFILPDSLN   74 (90)
T ss_pred             HhHHHHhCCCCEEEEEECCCCEEEEEEEEEcCceeEEEEEEEEEcCCCceeEcceEEEeCCEEEEEEcCCcCC
Confidence            6789999999999999999999999999999999999999999877767889999999999999999999863

Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Sm subunit D1 heterodimerizes with subunit D2 and three such heterodimers form a hexameric ring structure with alternating D1 and D2 subunits. The D1 - D2 heterodimer also assembles into a heptameric ring containing DB, D3, E, F, and G subunits. Sm-like proteins exist in archaea as well as prokaryotes which form heptameric and hexameric ring structures similar to those found in eukaryotes.

>cd01733 LSm10 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation

Probab=99.91  E-value=4.5e-24  Score=130.70  Aligned_cols=73  Identities=26%  Similarity=0.302  Sum_probs=67.4

Q ss_pred             CCCCcHHHHhhcCCCEEEEEEcCccEEEEEEEEecCCcceEEcceEEEecCeeeeeeceEEEeCCcEEEEEcC
Q psy6372           5 LPCNPKPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTGKLGEVLIRCNNILYIRGA   77 (88)
Q Consensus         5 ~~~~p~~~L~~~i~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~d~~e~~~~~~~~~~~~v~IrG~~I~~I~~~   77 (88)
                      ....+..||+++.|++|.|+|+||.+|+|+|.++|++||++|+||++..+++...+++.+||||++|+||++|
T Consensus         6 ~~~tl~~~L~~l~g~~V~VeLKng~~~~G~L~~vD~~MNl~L~~~~~~~~~~~~~~~~~v~IRG~nI~yI~lP   78 (78)
T cd01733           6 LENTLIILLQGLQGKVVTVELRNETTVTGRIASVDAFMNIRLAKVTIIDRNGKQVQVEEIMVTGRNIRYVHIP   78 (78)
T ss_pred             hhchHHHHHHHCCCCEEEEEECCCCEEEEEEEEEcCCceeEEEEEEEEcCCCceeECCcEEEECCEEEEEEcC
Confidence            4567789999999999999999999999999999999999999999886665667899999999999999987

Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. LSm10 is an SmD1-like protein which is thought to bind U7 snRNA along with LSm11 and five other Sm subunits to form a 7-member ring structure. LSm10 and the U7 snRNP of which it is a part are thought to play an important role in histone mRNA 3' processing.

>cd01719 Sm_G The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation

Probab=99.91  E-value=1.1e-23  Score=127.23  Aligned_cols=71  Identities=30%  Similarity=0.387  Sum_probs=65.7

Q ss_pred             cHHHHhhcCCCEEEEEEcCccEEEEEEEEecCCcceEEcceEEEecCeeeeeeceEEEeCCcEEEEEcCCC
Q psy6372           9 PKPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTGKLGEVLIRCNNILYIRGAEE   79 (88)
Q Consensus         9 p~~~L~~~i~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~d~~e~~~~~~~~~~~~v~IrG~~I~~I~~~d~   79 (88)
                      |.++|+++++|+|.|+|++|+.|.|+|.+||+|||++|+||.|...+...+.+|.++|||++|++|.+.|.
T Consensus         1 ~~~~L~~~i~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~~~~E~~~~~~~~~lg~v~IRG~~I~~i~~~~~   71 (72)
T cd01719           1 HPPELKKYMDKKLSLKLNGNRKVSGILRGFDPFMNLVLDDAVEVNSGGEKNNIGMVVIRGNSIVMLEALER   71 (72)
T ss_pred             CchhhHHhCCCeEEEEECCCeEEEEEEEEEcccccEEeccEEEEccCCceeEeceEEECCCEEEEEEcccc
Confidence            56789999999999999999999999999999999999999998766668899999999999999997753

Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Sm subunit G binds subunits E and F to form a trimer which then assembles onto snRNA along with the D1/D2 and D3/B heterodimers forming a seven-membered ring structure. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes.

>cd01732 LSm5 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation

Probab=99.90  E-value=2e-23  Score=127.28  Aligned_cols=70  Identities=26%  Similarity=0.385  Sum_probs=64.8

Q ss_pred             CCcHHHHhhcCCCEEEEEEcCccEEEEEEEEecCCcceEEcceEEEe---cCeeeeeeceEEEeCCcEEEEEc
Q psy6372           7 CNPKPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEII---DGHCTGKLGEVLIRCNNILYIRG   76 (88)
Q Consensus         7 ~~p~~~L~~~i~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~d~~e~~---~~~~~~~~~~v~IrG~~I~~I~~   76 (88)
                      ..|+++|+++++++|.|++++|+.+.|+|.+||+|||++|+||.|..   +++..+.+|.++|||++|.+|++
T Consensus         2 ~~P~~~L~~~~~~~V~V~l~~gr~~~G~L~g~D~~mNlvL~da~E~~~~~~~~~~~~lg~v~iRG~nV~~i~p   74 (76)
T cd01732           2 LLPLELIDKCIGSRIWIVMKSDKEFVGTLLGFDDYVNMVLEDVTEYEITPEGRKITKLDQILLNGNNICMLVP   74 (76)
T ss_pred             cChHHHHHHhCCCEEEEEECCCeEEEEEEEEeccceEEEEccEEEEEEcCCCceeeEcCeEEEeCCeEEEEEC
Confidence            36999999999999999999999999999999999999999999986   44456889999999999999985

Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. LSm4 is one of at least seven subunits that assemble onto U6 snRNA to form a seven-membered ring structure. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes.

>cd01725 LSm2 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation

Probab=99.90  E-value=2.3e-23  Score=128.24  Aligned_cols=75  Identities=23%  Similarity=0.286  Sum_probs=66.5

Q ss_pred             cHHHHhhcCCCEEEEEEcCccEEEEEEEEecCCcceEEcceEEEecCe--eeeeeceEEEeCCcEEEEEcCCCCCcc
Q psy6372           9 PKPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGH--CTGKLGEVLIRCNNILYIRGAEEGDEE   83 (88)
Q Consensus         9 p~~~L~~~i~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~d~~e~~~~~--~~~~~~~v~IrG~~I~~I~~~d~~~~~   83 (88)
                      |+.||+++.|++|+|+|+||.+|+|+|.++|+|||++|+||++..++.  ....++.++|||++|+||++||+..|.
T Consensus         2 ~~~fL~~l~g~~V~VeLKng~~~~G~L~~vD~~MNi~L~n~~~~~~~~~~~~~~~~~v~IRG~~I~~I~lp~~~i~~   78 (81)
T cd01725           2 FFSFFKTLVGKEVTVELKNDLSIRGTLHSVDQYLNIKLTNISVTDPEKYPHMLSVKNCFIRGSVVRYVQLPADEVDT   78 (81)
T ss_pred             hhHHHHhCCCCEEEEEECCCcEEEEEEEEECCCcccEEEEEEEEcCCCcccccccCeEEEECCEEEEEEeChhHcCc
Confidence            789999999999999999999999999999999999999998774322  245678999999999999999987654

Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. LSm2 is one of at least seven subunits that assemble onto U6 snRNA to form a seven-membered ring structure. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes.

>cd01730 LSm3 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation

Probab=99.89  E-value=1.1e-22  Score=125.21  Aligned_cols=69  Identities=22%  Similarity=0.347  Sum_probs=62.8

Q ss_pred             CcHHHHhhcCCCEEEEEEcCccEEEEEEEEecCCcceEEcceEEEecC-------------eeeeeeceEEEeCCcEEEE
Q psy6372           8 NPKPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDG-------------HCTGKLGEVLIRCNNILYI   74 (88)
Q Consensus         8 ~p~~~L~~~i~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~d~~e~~~~-------------~~~~~~~~v~IrG~~I~~I   74 (88)
                      .|+++|+.+++++|.|+|++|+.+.|+|.+||+|||++|+||.|.+.+             ...+.+|.+||||++|++|
T Consensus         1 ~pl~~l~~~~~k~V~V~l~~gr~~~G~L~~fD~~mNlvL~d~~E~~~~~~~~~~~~~~~~~~~~r~lg~~~iRGd~Vv~i   80 (82)
T cd01730           1 EPLDLIRLSLDERVYVKLRGDRELRGRLHAYDQHLNMILGDVEETITTVEIDEETYEEIVKTTKRNIPMLFVRGDSVILV   80 (82)
T ss_pred             CchHHHHHhCCCEEEEEECCCCEEEEEEEEEccceEEeccceEEEeecccccccccccccceeEEEcCeEEEeCCEEEEE
Confidence            489999999999999999999999999999999999999999998632             1467899999999999998


Q ss_pred             Ec
Q psy6372          75 RG   76 (88)
Q Consensus        75 ~~   76 (88)
                      .+
T Consensus        81 ~~   82 (82)
T cd01730          81 SP   82 (82)
T ss_pred             CC
Confidence            63

Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. LSm3 is one of at least seven subunits that assemble onto U6 snRNA to form a seven-membered ring structure. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes.

>KOG3482|consensus

Probab=99.89  E-value=4.9e-23  Score=123.69  Aligned_cols=77  Identities=70%  Similarity=1.142  Sum_probs=74.1

Q ss_pred             CCCCCCCCcHHHHhhcCCCEEEEEEcCccEEEEEEEEecCCcceEEcceEEEecCeeeeeeceEEEeCCcEEEEEcC
Q psy6372           1 MSTPLPCNPKPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTGKLGEVLIRCNNILYIRGA   77 (88)
Q Consensus         1 m~~~~~~~p~~~L~~~i~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~d~~e~~~~~~~~~~~~v~IrG~~I~~I~~~   77 (88)
                      ||+++|.+|.+||+.+.||+|.|+|+.|.+|.|+|++.|.+||+.|.+|+|..+|.....+|.++||-+||.||.-.
T Consensus         1 ~~a~~PvNPKpFL~~l~gk~V~vkLKwg~eYkG~LvsvD~YmNlqL~~~eE~idG~~~g~lGEilIRCNNvlyi~gv   77 (79)
T KOG3482|consen    1 SSAKQPVNPKPFLNGLTGKPVLVKLKWGQEYKGTLVSVDNYMNLQLANAEEYIDGVSTGNLGEILIRCNNVLYIRGV   77 (79)
T ss_pred             CCCcccCCchHHHhhccCCeEEEEEecCcEEEEEEEEecchhheehhhhhhhhcccccccceeEEEEeccEEEEecC
Confidence            79999999999999999999999999999999999999999999999999998998889999999999999999643

>COG1958 LSM1 Small nuclear ribonucleoprotein (snRNP) homolog [Transcription]

Probab=99.89  E-value=2.1e-22  Score=123.03  Aligned_cols=74  Identities=50%  Similarity=0.684  Sum_probs=65.2

Q ss_pred             CCCCCCcHHHHhhcCCCEEEEEEcCccEEEEEEEEecCCcceEEcceEEEe--cCee-eeeec-eEEEeCCcEEEEEc
Q psy6372           3 TPLPCNPKPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEII--DGHC-TGKLG-EVLIRCNNILYIRG   76 (88)
Q Consensus         3 ~~~~~~p~~~L~~~i~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~d~~e~~--~~~~-~~~~~-~v~IrG~~I~~I~~   76 (88)
                      ++....|+.+|+++++++|.|+|++|++|+|+|.+||+|||++|+||.+..  ++.. .+.++ .++|||++|++|.+
T Consensus         2 ~~~~~~~~~~l~~~~~~~V~V~lk~g~~~~G~L~~~D~~mNlvL~d~~e~~~~~~~~~~~~~~~~~~IRG~~I~~I~~   79 (79)
T COG1958           2 SMLGPLPLSFLKKLLNKRVLVKLKNGREYRGTLVGFDQYMNLVLDDVEEIISHDGEKNVRRLGGEVLIRGDNIVLISP   79 (79)
T ss_pred             CcccCCcHHHHHHhhCCEEEEEECCCCEEEEEEEEEccceeEEEeceEEEeccCCccccceeccEEEEECCcEEEEeC
Confidence            455678999999999999999999999999999999999999999999986  5544 34555 99999999999963

>PF01423 LSM: LSM domain ; InterPro: IPR001163 This family is found in Lsm (like-Sm) proteins and in bacterial Lsm-related Hfq proteins

Probab=99.89  E-value=2.5e-22  Score=118.41  Aligned_cols=66  Identities=44%  Similarity=0.577  Sum_probs=62.5

Q ss_pred             HHHhhcCCCEEEEEEcCccEEEEEEEEecCCcceEEcceEEEecCe-eeeeeceEEEeCCcEEEEEc
Q psy6372          11 PFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGH-CTGKLGEVLIRCNNILYIRG   76 (88)
Q Consensus        11 ~~L~~~i~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~d~~e~~~~~-~~~~~~~v~IrG~~I~~I~~   76 (88)
                      .+|++++|++|+|+|+||++|+|+|.+||+|||++|+||.+...+. +.++++.+||||++|++|++
T Consensus         1 ~~L~~~~g~~V~V~l~~g~~~~G~L~~~D~~~Nl~L~~~~~~~~~~~~~~~~~~~~irG~~I~~I~~   67 (67)
T PF01423_consen    1 NFLQKLIGKRVRVELKNGRTYRGTLVSFDQFMNLVLSDVTETIKNGPEKRSLGLVFIRGSNIRYISL   67 (67)
T ss_dssp             HHHHHTTTSEEEEEETTSEEEEEEEEEEETTEEEEEEEEEEEETTESEEEEEEEEEEEGGGEEEEEE
T ss_pred             ChhHHhCCcEEEEEEeCCEEEEEEEEEeechheEEeeeEEEEECCCCcEeECcEEEEECCEEEEEEC
Confidence            3799999999999999999999999999999999999999998776 88999999999999999975

In each case, the domain adopts a core structure consisting of an open beta-barrel with an SH3-like topology. Lsm (like-Sm) proteins have diverse functions, and are thought to be important modulators of RNA biogenesis and function [, ]. The Sm proteins form part of specific small nuclear ribonucleoproteins (snRNPs) that are involved in the processing of pre-mRNAs to mature mRNAs, and are a major component of the eukaryotic spliceosome. Most snRNPs consist of seven Sm proteins (B/B', D1, D2, D3, E, F and G) arranged in a ring on a uridine-rich sequence (Sm site), plus a small nuclear RNA (snRNA) (either U1, U2, U5 or U4/6) []. All Sm proteins contain a common sequence motif in two segments, Sm1 and Sm2, separated by a short variable linker []. In other snRNPs, certain Sm proteins are replaced with different Lsm proteins, such as with U7 snRNPs, in which the D1 and D2 Sm proteins are replaced with U7-specific Lsm10 and Lsm11 proteins, where Lsm11 plays a role in histone U7-specific RNA processing []. Lsm proteins are also found in archaebacteria, which do not have any splicing apparatus suggesting a more general role for Lsm proteins. The pleiotropic translational regulator Hfq (host factor Q) is a bacterial Lsm-like protein, which modulates the structure of numerous RNA molecules by binding preferentially to A/U-rich sequences in RNA []. Hfq forms an Lsm-like fold, however, unlike the heptameric Sm proteins, Hfq forms a homo-hexameric ring.; PDB: 1D3B_K 2Y9D_D 2Y9A_D 2Y9C_R 3VRI_C 2Y9B_K 3QUI_D 3M4G_H 3INZ_E 1U1S_C ....

>smart00651 Sm snRNP Sm proteins

Probab=99.88  E-value=3.1e-22  Score=117.89  Aligned_cols=66  Identities=45%  Similarity=0.646  Sum_probs=61.6

Q ss_pred             HHHhhcCCCEEEEEEcCccEEEEEEEEecCCcceEEcceEEEecC-eeeeeeceEEEeCCcEEEEEc
Q psy6372          11 PFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDG-HCTGKLGEVLIRCNNILYIRG   76 (88)
Q Consensus        11 ~~L~~~i~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~d~~e~~~~-~~~~~~~~v~IrG~~I~~I~~   76 (88)
                      .+|++++|++|+|+|+||+.+.|+|.+||+|||++|+||.+...+ ...++++.+||||++|++|++
T Consensus         1 ~~L~~~~~~~V~V~l~~g~~~~G~L~~~D~~~NlvL~~~~e~~~~~~~~~~~~~~~IrG~~I~~i~~   67 (67)
T smart00651        1 KFLKKLIGKRVLVELKNGREYRGTLKGFDQFMNLVLEDVEETVKDGEKKRKLGLVFIRGNNIVYIIL   67 (67)
T ss_pred             ChhHHhCCcEEEEEECCCcEEEEEEEEECccccEEEccEEEEecCCcEEeEeCCEEEcCCEEEEEeC
Confidence            379999999999999999999999999999999999999998665 578999999999999999974

small nuclear ribonucleoprotein particles (snRNPs) involved in pre-mRNA splicing

>cd01720 Sm_D2 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation

Probab=99.88  E-value=5.5e-22  Score=123.75  Aligned_cols=71  Identities=13%  Similarity=0.197  Sum_probs=63.0

Q ss_pred             CCcHHHHhhcC--CCEEEEEEcCccEEEEEEEEecCCcceEEcceEEEecCe-------------eeeeeceEEEeCCcE
Q psy6372           7 CNPKPFLNLLT--GKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGH-------------CTGKLGEVLIRCNNI   71 (88)
Q Consensus         7 ~~p~~~L~~~i--~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~d~~e~~~~~-------------~~~~~~~v~IrG~~I   71 (88)
                      ..|+++|+.++  +++|.|+|++|+.+.|+|.+||+|||++|+||.|.+.+.             ..+.+|.+||||++|
T Consensus         1 ~gPl~~L~~~~~~~~~V~V~lr~~r~~~G~L~~fD~hmNlvL~d~~E~~~~~~k~~~~~~~~~~~~~r~lg~v~iRGd~V   80 (87)
T cd01720           1 TGPLSLLTQAVKNNTQVLINCRNNKKLLGRVKAFDRHCNMVLENVKEMWTEVPKTGKGKKAKPVNKDRFISKMFLRGDSV   80 (87)
T ss_pred             CChHHHHHHHHcCCCEEEEEEcCCCEEEEEEEEecCccEEEEcceEEEeeccccccccccccceeeeeEcccEEEeCCEE
Confidence            36999999997  899999999999999999999999999999999975331             356789999999999


Q ss_pred             EEEEcC
Q psy6372          72 LYIRGA   77 (88)
Q Consensus        72 ~~I~~~   77 (88)
                      ++|...
T Consensus        81 v~Is~~   86 (87)
T cd01720          81 ILVLRN   86 (87)
T ss_pred             EEEecC
Confidence            999753

Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Sm subunit D2 heterodimerizes with subunit D1 and three such heterodimers form a hexameric ring structure with alternating D1 and D2 subunits. The D1 - D2 heterodimer also assembles into a heptameric ring containing D2, D3, E, F, and G subunits. Sm-like proteins exist in archaea as well as prokaryotes which form heptameric and hexameric ring structures similar to those found in eukaryotes.

>cd01729 LSm7 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation

Probab=99.87  E-value=8.8e-22  Score=121.21  Aligned_cols=68  Identities=28%  Similarity=0.335  Sum_probs=61.3

Q ss_pred             HHHhhcCCCEEEEEEcCccEEEEEEEEecCCcceEEcceEEEecC--------eeeeeeceEEEeCCcEEEEEcCC
Q psy6372          11 PFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDG--------HCTGKLGEVLIRCNNILYIRGAE   78 (88)
Q Consensus        11 ~~L~~~i~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~d~~e~~~~--------~~~~~~~~v~IrG~~I~~I~~~d   78 (88)
                      .-|.++++|+|+|+|++|+.|.|+|.+||+||||+|++|+|...+        ...+.+|.++|||++|.+|.+.+
T Consensus         5 ~~L~~~i~k~V~V~l~~gr~~~G~L~~~D~~mNlvL~~~~E~~~~~~~~~~~~~~~~~lG~v~iRG~nV~~i~~~~   80 (81)
T cd01729           5 LDLSKYVDKKIRVKFQGGREVTGILKGYDQLLNLVLDDTVEYLRDPDDPYKLTDKTRQLGLVVCRGTSVVLISPVD   80 (81)
T ss_pred             hhHHHhcCCeEEEEECCCcEEEEEEEEEcCcccEEecCEEEEEccCCcccccccceeEccEEEEcCCEEEEEecCC
Confidence            449999999999999999999999999999999999999998543        24688999999999999998765

Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. LSm7 is one of at least seven subunits that assemble onto U6 snRNA to form a seven-membered ring structure. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes.

>cd00600 Sm_like The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation

Probab=99.85  E-value=7.1e-21  Score=110.65  Aligned_cols=63  Identities=41%  Similarity=0.523  Sum_probs=58.8

Q ss_pred             HhhcCCCEEEEEEcCccEEEEEEEEecCCcceEEcceEEEecCeeeeeeceEEEeCCcEEEEE
Q psy6372          13 LNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTGKLGEVLIRCNNILYIR   75 (88)
Q Consensus        13 L~~~i~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~d~~e~~~~~~~~~~~~v~IrG~~I~~I~   75 (88)
                      |++++|++|+|+|+||+.|.|+|.+||+|||++|+||.+...+...+.++.+||||++|++|.
T Consensus         1 l~~~~g~~V~V~l~~g~~~~G~L~~~D~~~Ni~L~~~~~~~~~~~~~~~~~~~irG~~I~~I~   63 (63)
T cd00600           1 LKDLVGKTVRVELKDGRVLEGVLVAFDKYMNLVLDDVEETIKEGKKRVLGLVLIRGDNVRLVT   63 (63)
T ss_pred             ChHHCCCEEEEEECCCcEEEEEEEEECCCCCEEECCEEEEecCCcEEECCeEEEECCEEEEEC
Confidence            578899999999999999999999999999999999999876567899999999999999984

Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes.

>cd01718 Sm_E The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation

Probab=99.85  E-value=1.4e-20  Score=115.54  Aligned_cols=73  Identities=23%  Similarity=0.323  Sum_probs=64.5

Q ss_pred             CCCCCcHHHHhhcCCC--EEEEEEc--CccEEEEEEEEecCCcceEEcceEEEec-CeeeeeeceEEEeCCcEEEEEc
Q psy6372           4 PLPCNPKPFLNLLTGK--SVICKLK--WGHEYKGILVSTDGYMNCQLASTEEIID-GHCTGKLGEVLIRCNNILYIRG   76 (88)
Q Consensus         4 ~~~~~p~~~L~~~i~k--~V~V~L~--~g~~~~G~L~~~D~~mNlvL~d~~e~~~-~~~~~~~~~v~IrG~~I~~I~~   76 (88)
                      ++-..|+..|.+++++  +|.|+++  +|+.+.|+|.|||+|||++|+||.|... +...+.+|.++|||++|.+|++
T Consensus         2 ~~~~~P~~~l~~~l~~~~~V~V~l~~~~g~~~~G~L~gfD~~mNlvL~d~~E~~~~~~~~~~lG~iliRGnnV~~I~p   79 (79)
T cd01718           2 KVMVQPINLIFRFLQSKQRVQIWLYEQTDLRIEGVIIGFDEYMNLVLDDAEEVHLKTKTRKPLGRILLKGDNITLIQN   79 (79)
T ss_pred             ccccCCHHHHHHHHccCcEEEEEEEeCCCcEEEEEEEEEccceeEEEcCEEEEecCCceEeEcCcEEEeCCEEEEEcC
Confidence            3456799999999999  7888887  8999999999999999999999999864 4567889999999999999973

Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Sm subunit E binds subunits F and G to form a trimer which then assembles onto snRNA along with the D1/D2 and D3/B heterodimers forming a seven-membered ring structure. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes.

>cd01717 Sm_B The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation

Probab=99.85  E-value=1.2e-20  Score=115.33  Aligned_cols=66  Identities=26%  Similarity=0.283  Sum_probs=59.5

Q ss_pred             HHHhhcCCCEEEEEEcCccEEEEEEEEecCCcceEEcceEEEecC----------eeeeeeceEEEeCCcEEEEEc
Q psy6372          11 PFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDG----------HCTGKLGEVLIRCNNILYIRG   76 (88)
Q Consensus        11 ~~L~~~i~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~d~~e~~~~----------~~~~~~~~v~IrG~~I~~I~~   76 (88)
                      +-|.+++|++|+|+|++|+.+.|+|.+||+|||++|+||.|.+..          ...+.+|+++|||++|++|.+
T Consensus         3 ~~l~~~l~~~V~V~l~dgR~~~G~L~~~D~~~NlVL~~~~E~~~~~~~~~~~~~~~~~r~lG~v~iRG~~Vv~i~v   78 (79)
T cd01717           3 SKMLQLINYRLRVTLQDGRQFVGQFLAFDKHMNLVLSDCEEFRKVKKKKSKNSEREEKRTLGLVLLRGENIVSMTV   78 (79)
T ss_pred             chhHHHcCCEEEEEECCCcEEEEEEEEEcCccCEEcCCEEEEEeccccccccccCcceeEeeeEEEcCCEEEEEEE
Confidence            468899999999999999999999999999999999999997521          246889999999999999974

Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Sm subunit B heterodimerizes with subunit D3 and three such heterodimers form a hexameric ring structure with alternating B and D3 subunits. The D3 - B heterodimer also assembles into a heptameric ring containing D1, D2, E, F, and G subunits. Sm-like proteins exist in archaea as well as prokaryotes which form heptameric and hexameric ring structures similar to those found in eukaryotes.

>cd01727 LSm8 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation

Probab=99.85  E-value=1.7e-20  Score=113.48  Aligned_cols=69  Identities=26%  Similarity=0.194  Sum_probs=62.1

Q ss_pred             HHHhhcCCCEEEEEEcCccEEEEEEEEecCCcceEEcceEEEec----CeeeeeeceEEEeCCcEEEEEcCCC
Q psy6372          11 PFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIID----GHCTGKLGEVLIRCNNILYIRGAEE   79 (88)
Q Consensus        11 ~~L~~~i~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~d~~e~~~----~~~~~~~~~v~IrG~~I~~I~~~d~   79 (88)
                      +.|.++++++|+|.|++|+.|.|+|.+||+|||++|++|.|...    +...+.+|.++|||++|.+|.+.|+
T Consensus         2 ~~L~~~l~~~V~V~l~dgr~~~G~L~~~D~~~NlvL~~~~E~~~~~~~~~~~~~lG~~~iRG~~I~~i~~~d~   74 (74)
T cd01727           2 STLEDYLNKTVSVITVDGRVIVGTLKGFDQATNLILDDSHERVYSSDEGVEQVVLGLYIIRGDNIAVVGEIDE   74 (74)
T ss_pred             hhHHHhcCCEEEEEECCCcEEEEEEEEEccccCEEccceEEEEecCCCCceeeEeceEEECCCEEEEEEccCC
Confidence            56899999999999999999999999999999999999998742    3356789999999999999998764

Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. LSm8 is one of at least seven subunits that assemble onto U6 snRNA to form a seven-membered ring structure. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes.

>cd01728 LSm1 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation

Probab=99.84  E-value=4.9e-20  Score=111.87  Aligned_cols=68  Identities=29%  Similarity=0.270  Sum_probs=60.7

Q ss_pred             cHHHHhhcCCCEEEEEEcCccEEEEEEEEecCCcceEEcceEEEe-cC-e-eeeeeceEEEeCCcEEEEEc
Q psy6372           9 PKPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEII-DG-H-CTGKLGEVLIRCNNILYIRG   76 (88)
Q Consensus         9 p~~~L~~~i~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~d~~e~~-~~-~-~~~~~~~v~IrG~~I~~I~~   76 (88)
                      ++..|.++++|+|.|.|++|+.|.|+|.+||+|||++|+||.|.. .+ + ..+.+|.++|||++|.+|..
T Consensus         3 ~~~~L~~~l~k~v~V~l~~gr~~~G~L~~fD~~~NlvL~d~~E~~~~~~~~~~~~lG~~viRG~~V~~ig~   73 (74)
T cd01728           3 GTASLVDDLDKKVVVLLRDGRKLIGILRSFDQFANLVLQDTVERIYVGDKYGDIPRGIFIIRGENVVLLGE   73 (74)
T ss_pred             chHHHHHhcCCEEEEEEcCCeEEEEEEEEECCcccEEecceEEEEecCCccceeEeeEEEEECCEEEEEEc
Confidence            467899999999999999999999999999999999999999874 22 1 46789999999999999974

Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. LSm1 is one of at least seven subunits that assemble onto U6 snRNA to form a seven-membered ring structure. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes.

>KOG1783|consensus

Probab=99.82  E-value=2.4e-21  Score=116.39  Aligned_cols=74  Identities=43%  Similarity=0.743  Sum_probs=70.5

Q ss_pred             CCCCcHHHHhhcCCCEEEEEEcCccEEEEEEEEecCCcceEEcceEEEecCeeeeeeceEEEeCCcEEEEEcCC
Q psy6372           5 LPCNPKPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTGKLGEVLIRCNNILYIRGAE   78 (88)
Q Consensus         5 ~~~~p~~~L~~~i~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~d~~e~~~~~~~~~~~~v~IrG~~I~~I~~~d   78 (88)
                      ....|.+||++.+||+|.|+|.+|..|+|+|.++|.+||+.|+.+.+..+|+.+++++..||||++|.||....
T Consensus         3 ~~~~~~~fl~~iiGr~V~VKl~sgvdyrG~l~~lDgymNiaLe~tee~~ngql~n~ygdaFirGnnVlyIs~~~   76 (77)
T KOG1783|consen    3 EGSMPGEFLKAIIGRTVVVKLNSGVDYRGTLVCLDGYMNIALESTEEYVNGQLKNKYGDAFIRGNNVLYISTQK   76 (77)
T ss_pred             cccCcHHHHHHHhCCeEEEEecCCccccceehhhhhHHHHHHHHHHHHhcCcccccccceeeccccEEEEEecc
Confidence            66789999999999999999999999999999999999999999999999999999999999999999998653

>cd06168 LSm9 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation

Probab=99.81  E-value=2.2e-19  Score=109.20  Aligned_cols=66  Identities=26%  Similarity=0.278  Sum_probs=60.7

Q ss_pred             HHHhhcCCCEEEEEEcCccEEEEEEEEecCCcceEEcceEEEecC------eeeeeeceEEEeCCcEEEEEc
Q psy6372          11 PFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDG------HCTGKLGEVLIRCNNILYIRG   76 (88)
Q Consensus        11 ~~L~~~i~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~d~~e~~~~------~~~~~~~~v~IrG~~I~~I~~   76 (88)
                      +.|++++|++|+|+|+|||.|.|+|.+||++||++|+||.|.+..      ...+.+|+++|||++|.+|..
T Consensus         3 ~~L~~~l~~~v~V~l~dgR~~~G~l~~~D~~~NivL~~~~E~~~~~~~~~~~~~r~lGlv~IrG~~Iv~i~v   74 (75)
T cd06168           3 QKLRSLLGRTMRIHMTDGRTLVGVFLCTDRDCNIILGSAQEYRPPPDSFSPTEPRVLGLVMIPGHHIVSIEV   74 (75)
T ss_pred             hHHHHhcCCeEEEEEcCCeEEEEEEEEEcCCCcEEecCcEEEEcccCccCCccEEEeeeEEEeCCeEEEEEE
Confidence            568999999999999999999999999999999999999998632      468899999999999999975

Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. LSm9 proteins have a single Sm-like domain structure. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes.

>PTZ00138 small nuclear ribonucleoprotein; Provisional

Probab=99.78  E-value=1.8e-18  Score=108.28  Aligned_cols=74  Identities=24%  Similarity=0.297  Sum_probs=62.8

Q ss_pred             CCCCCcHHHHhhcCCC--EEEEEEcC--ccEEEEEEEEecCCcceEEcceEEEec-CeeeeeeceEEEeCCcEEEEEcC
Q psy6372           4 PLPCNPKPFLNLLTGK--SVICKLKW--GHEYKGILVSTDGYMNCQLASTEEIID-GHCTGKLGEVLIRCNNILYIRGA   77 (88)
Q Consensus         4 ~~~~~p~~~L~~~i~k--~V~V~L~~--g~~~~G~L~~~D~~mNlvL~d~~e~~~-~~~~~~~~~v~IrG~~I~~I~~~   77 (88)
                      +.-..|+.++.+++++  +|.|++.+  ++.+.|+|.+||+|||++|+||+|... +...+.+|.++|||++|.+|.+.
T Consensus        10 ~~~~~P~~~~~~~~~~~~~V~i~l~~~~~r~~~G~L~gfD~~mNlVL~d~~E~~~~~~~~~~lG~ilIRGnnV~~I~~~   88 (89)
T PTZ00138         10 KIMTQPINQIFRFFTEKTRVQIWLYDHPNLRIEGKILGFDEYMNMVLDDAEEVYTKKNTRKDLGRILLKGDNITLIMAA   88 (89)
T ss_pred             eeecCCHHHHHHHhcCCcEEEEEEEeCCCcEEEEEEEEEcccceEEEccEEEEecCCceeeEcCeEEEcCCEEEEEEcC
Confidence            3456799999999875  47777767  599999999999999999999999854 34578999999999999999753

>KOG1780|consensus

Probab=99.76  E-value=2.4e-18  Score=103.68  Aligned_cols=68  Identities=31%  Similarity=0.386  Sum_probs=62.0

Q ss_pred             HHhhcCCCEEEEEEcCccEEEEEEEEecCCcceEEcceEEEecCeeeeeeceEEEeCCcEEEEEcCCC
Q psy6372          12 FLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTGKLGEVLIRCNNILYIRGAEE   79 (88)
Q Consensus        12 ~L~~~i~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~d~~e~~~~~~~~~~~~v~IrG~~I~~I~~~d~   79 (88)
                      .|+++.+|++.++|..||..+|.|.+||.|||++|+++.|.........++.++|||++|+.+...+.
T Consensus         8 eLkkymdKki~lklnG~r~v~GiLrGyD~FmNiVlde~vE~~~~~~~~~ig~~vIrgnsiv~~eaL~~   75 (77)
T KOG1780|consen    8 ELKKYMDKKIVLKLNGGRKVTGILRGYDPFMNIVLDETVEPNGDGDKNNIGMVVIRGNSIVMVEALER   75 (77)
T ss_pred             hHHHhhhheEEEEeCCCcEEEEEEeccchHHhhhhhhceeecCcCCcceeeeEEEeccEEEEEeeccc
Confidence            79999999999999999999999999999999999999998544457889999999999999987653

>KOG3293|consensus

Probab=99.73  E-value=6.3e-18  Score=110.48  Aligned_cols=75  Identities=29%  Similarity=0.394  Sum_probs=69.7

Q ss_pred             CcHHHHhhcCCCEEEEEEcCccEEEEEEEEecCCcceEEcceEEEe-cCeeeeeeceEEEeCCcEEEEEcCCCCCc
Q psy6372           8 NPKPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEII-DGHCTGKLGEVLIRCNNILYIRGAEEGDE   82 (88)
Q Consensus         8 ~p~~~L~~~i~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~d~~e~~-~~~~~~~~~~v~IrG~~I~~I~~~d~~~~   82 (88)
                      .|+.+|..+-++++.|+|+||.+|.|-|+.||.+|||.|.++.++. ++.+...+++++|||++|.|+.+||+..+
T Consensus         2 lPLsLL~~aq~~pmlvELKNget~nGhL~~cD~wMNl~L~~Vi~ts~Dgdkf~r~pEcYirGttIkylri~d~iid   77 (134)
T KOG3293|consen    2 LPLSLLKTAQNHPMLVELKNGETYNGHLVNCDNWMNLHLREVICTSEDGDKFFRMPECYIRGTTIKYLRIPDEIID   77 (134)
T ss_pred             cchhHHHhcCCCeEEEEecCCCEecceeecchhhhhcchheeEEeccCCCceeecceeEEecceeEEEeccHHHHH
Confidence            5999999999999999999999999999999999999999999985 56678889999999999999999997643

>KOG3460|consensus

Probab=99.70  E-value=5.5e-18  Score=104.22  Aligned_cols=74  Identities=22%  Similarity=0.289  Sum_probs=66.2

Q ss_pred             CCcHHHHhhcCCCEEEEEEcCccEEEEEEEEecCCcceEEcceEEEe---cC----------eeeeeeceEEEeCCcEEE
Q psy6372           7 CNPKPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEII---DG----------HCTGKLGEVLIRCNNILY   73 (88)
Q Consensus         7 ~~p~~~L~~~i~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~d~~e~~---~~----------~~~~~~~~v~IrG~~I~~   73 (88)
                      ..|+++|+-.++.+|.|+++++++++|+|++||+|.|++|.|+.++.   ++          ...+.+..+||||++|.+
T Consensus         4 ~ePldllrlsLdErVyVKlr~drel~G~L~afD~HlNmvL~d~eetit~~e~~E~~~e~~~k~~~r~~emlFvRGd~Vil   83 (91)
T KOG3460|consen    4 EEPLDLLRLSLDERVYVKLRSDRELRGTLHAFDEHLNMVLGDVEETITTVEIDEDTYEEIVKTTKRTVEMLFVRGDGVIL   83 (91)
T ss_pred             cccHHHHhhcccceEEEEecCChhhhcchhhhHHhhhhhhhhhhheEEEeeccchhHHHHHhhhhcceeEEEEeCCeEEE
Confidence            57999999999999999999999999999999999999999999863   11          256789999999999999


Q ss_pred             EEcCCCC
Q psy6372          74 IRGAEEG   80 (88)
Q Consensus        74 I~~~d~~   80 (88)
                      |.+|-..
T Consensus        84 vspp~~~   90 (91)
T KOG3460|consen   84 VSPPLRL   90 (91)
T ss_pred             EcCcccC
Confidence            9988653

>KOG3448|consensus

Probab=99.68  E-value=1.6e-16  Score=98.73  Aligned_cols=72  Identities=24%  Similarity=0.309  Sum_probs=63.9

Q ss_pred             HHHHhhcCCCEEEEEEcCccEEEEEEEEecCCcceEEcceEEEecCe--eeeeeceEEEeCCcEEEEEcCCCCC
Q psy6372          10 KPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGH--CTGKLGEVLIRCNNILYIRGAEEGD   81 (88)
Q Consensus        10 ~~~L~~~i~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~d~~e~~~~~--~~~~~~~v~IrG~~I~~I~~~d~~~   81 (88)
                      .+|+++++|+.|.|+|+|+-.+.|+|.++|+|.|+.|.|.....+.+  .-.++..+||||+.|+||.+|.+.-
T Consensus         4 ysfFkslvg~~V~VeLKnd~~i~GtL~svDqyLNlkL~di~v~d~~kyPhm~Sv~ncfIRGSvvrYv~l~kd~v   77 (96)
T KOG3448|consen    4 YSFFKSLVGKEVVVELKNDLSICGTLHSVDQYLNLKLTDISVTDPDKYPHMLSVKNCFIRGSVVRYVQLPKDAV   77 (96)
T ss_pred             HHHHHHhcCCeEEEEEcCCcEEEEEecccchhheeEEeeeEeeCcccCCCeeeeeeEEEeccEEEEEEeChhHH
Confidence            47899999999999999999999999999999999999999774432  3567789999999999999998754

>KOG3172|consensus

Probab=99.66  E-value=4.2e-16  Score=99.95  Aligned_cols=73  Identities=26%  Similarity=0.388  Sum_probs=68.0

Q ss_pred             CCCcHHHHhhcCCCEEEEEEcCccEEEEEEEEecCCcceEEcceEEEecCeeeeeeceEEEeCCcEEEEEcCC
Q psy6372           6 PCNPKPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTGKLGEVLIRCNNILYIRGAE   78 (88)
Q Consensus         6 ~~~p~~~L~~~i~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~d~~e~~~~~~~~~~~~v~IrG~~I~~I~~~d   78 (88)
                      ...|+.+|+..-|.-|++++..|..|+|+|...+++||++|+|++.+..+.....+++|||||++|+|+.+||
T Consensus         3 ~gvpiKlLhEaqGhIVt~Et~tGe~YRGkliEaeDnmNcql~di~vT~~dg~vs~le~V~IRGS~IRFlvlPd   75 (119)
T KOG3172|consen    3 VGVPIKLLHEAQGHIVTVETKTGEVYRGKLIEAEDNMNCQLRDITVTARDGRVSQLEQVFIRGSKIRFLVLPD   75 (119)
T ss_pred             cccceeeeecccCcEEEEEecCCceeeeeeEEeccccccEEEEEEEEccCCcceeeeeEEEecCeEEEEECch
Confidence            4579999999999999999999999999999999999999999998855556889999999999999999997

>KOG1775|consensus

Probab=99.63  E-value=5e-16  Score=94.24  Aligned_cols=76  Identities=25%  Similarity=0.378  Sum_probs=67.9

Q ss_pred             CCCCCCcHHHHhhcCCCEEEEEEcCccEEEEEEEEecCCcceEEcceEEEe---cCeeeeeeceEEEeCCcEEEEEcCC
Q psy6372           3 TPLPCNPKPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEII---DGHCTGKLGEVLIRCNNILYIRGAE   78 (88)
Q Consensus         3 ~~~~~~p~~~L~~~i~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~d~~e~~---~~~~~~~~~~v~IrG~~I~~I~~~d   78 (88)
                      +.....|++++.+++|.+|.|.+++++++.|+|.+||+|.|++|+|++|+-   +|+...+++++++.|++|....+.-
T Consensus         2 n~~~llPlEliDkcIgski~iimksdkE~~GtL~GFDd~VNmvLeDvtEye~~~egr~~tk~~~iLLnGNni~mLvPGG   80 (84)
T KOG1775|consen    2 NPSTLLPLELIDKCIGSKIWIIMKSDKEFVGTLVGFDDFVNMVLEDVTEYEITPEGRRMTKLDQILLNGNNITMLVPGG   80 (84)
T ss_pred             ChhhcccHHHHHHhcCceEEEEEccCceeeeEEechHHHHHHHHHhhhheeeCCCcceeeeeeeeeecCCcEEEEecCC
Confidence            345678999999999999999999999999999999999999999999872   4556778999999999999987654

>KOG3428|consensus

Probab=99.57  E-value=2.2e-14  Score=91.99  Aligned_cols=72  Identities=29%  Similarity=0.302  Sum_probs=66.6

Q ss_pred             cHHHHhhcCCCEEEEEEcCccEEEEEEEEecCCcceEEcceEEEecCeeeeeeceEEEeCCcEEEEEcCCCCC
Q psy6372           9 PKPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTGKLGEVLIRCNNILYIRGAEEGD   81 (88)
Q Consensus         9 p~~~L~~~i~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~d~~e~~~~~~~~~~~~v~IrG~~I~~I~~~d~~~   81 (88)
                      ...||+++.+.+|+|+|+||+..+|++.++|.+||..|.++.-+.+| ++.++...+|||++|+|+.+||.-.
T Consensus         3 lvr~L~kl~~e~vtIeLkngt~v~G~I~~Vd~~Mn~~l~~v~~t~~~-~pv~l~~lsirgnniRy~~lpD~l~   74 (109)
T KOG3428|consen    3 LVRFLKKLLNERVTIELKNGTIVHGTIDSVDVQMNTHLKHVKMTVKG-EPVRLDTLSIRGNNIRYYILPDSLN   74 (109)
T ss_pred             HHHHHHHhhCCeEEEEecCCcEEeeeEEEEEhhheeEEEEEEEecCC-CceeEEEEEeecceEEEEEccCCcC
Confidence            46799999999999999999999999999999999999999988777 6789999999999999999998753

>KOG1781|consensus

Probab=99.52  E-value=1.3e-15  Score=96.30  Aligned_cols=73  Identities=32%  Similarity=0.317  Sum_probs=64.2

Q ss_pred             HHHHhhcCCCEEEEEEcCccEEEEEEEEecCCcceEEcceEEE-ec-------CeeeeeeceEEEeCCcEEEEEcCCCCC
Q psy6372          10 KPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEI-ID-------GHCTGKLGEVLIRCNNILYIRGAEEGD   81 (88)
Q Consensus        10 ~~~L~~~i~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~d~~e~-~~-------~~~~~~~~~v~IrG~~I~~I~~~d~~~   81 (88)
                      .-.|.++++|+|+|++..||+..|+|.+||+.||++|+++.|+ ++       +...|++|++.+||..++.|.+.|.-|
T Consensus        19 ilDLsky~Dk~Irvkf~GGr~~sGiLkGyDqLlNlVLDd~vEylrdpdd~~~~~~~tR~LGLvV~RGTalvlisp~dG~e   98 (108)
T KOG1781|consen   19 ILDLSKYLDKKIRVKFTGGREASGILKGYDQLLNLVLDDTVEYLRDPDDPYKLTDETRKLGLVVCRGTALVLISPADGSE   98 (108)
T ss_pred             HhhHHHhhccceEEEeecCceeeeehhhHHHHHHHHHHHHHHHhcCCCCccchhhhhheeeeEEEcccEEEEEcCCcchh
Confidence            4468999999999999999999999999999999999999986 22       125699999999999999999887655


Q ss_pred             c
Q psy6372          82 E   82 (88)
Q Consensus        82 ~   82 (88)
                      |
T Consensus        99 ~   99 (108)
T KOG1781|consen   99 E   99 (108)
T ss_pred             h
Confidence            4

>KOG1784|consensus

Probab=99.34  E-value=9.9e-13  Score=82.17  Aligned_cols=72  Identities=24%  Similarity=0.183  Sum_probs=64.4

Q ss_pred             HHHhhcCCCEEEEEEcCccEEEEEEEEecCCcceEEcceEEEe----cCeeeeeeceEEEeCCcEEEEEcCCCCCc
Q psy6372          11 PFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEII----DGHCTGKLGEVLIRCNNILYIRGAEEGDE   82 (88)
Q Consensus        11 ~~L~~~i~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~d~~e~~----~~~~~~~~~~v~IrG~~I~~I~~~d~~~~   82 (88)
                      +-|.++++++|.|.+.|||.+.|+|.+||+..||.|+++-+..    .+.....+|..+|||+||..|.+.||+-+
T Consensus         3 s~L~~y~n~~V~vIt~DGr~ivgsLkGFDq~tNlii~~~heRi~s~~~gv~q~~lGlyiirgeNva~ig~iDEe~d   78 (96)
T KOG1784|consen    3 STLEDYMNQRVSVITNDGRVIVGSLKGFDQTTNLIIDESHERIFSETEGVEQIVLGLYIIRGENVAVIGEIDEELD   78 (96)
T ss_pred             hhHHHHhhceEEEEecCCeEEEEEeccccccceeeehhhHhhhhhhhcchhheeeEEEEEecCccceeeecchhhh
Confidence            4588999999999999999999999999999999999999863    35567788999999999999999988754

>KOG1774|consensus

Probab=99.30  E-value=2.6e-12  Score=78.89  Aligned_cols=71  Identities=28%  Similarity=0.381  Sum_probs=58.7

Q ss_pred             CCcHHHHhhcCCC--EEEEEEcC--ccEEEEEEEEecCCcceEEcceEEEe-cCeeeeeeceEEEeCCcEEEEEcC
Q psy6372           7 CNPKPFLNLLTGK--SVICKLKW--GHEYKGILVSTDGYMNCQLASTEEII-DGHCTGKLGEVLIRCNNILYIRGA   77 (88)
Q Consensus         7 ~~p~~~L~~~i~k--~V~V~L~~--g~~~~G~L~~~D~~mNlvL~d~~e~~-~~~~~~~~~~v~IrG~~I~~I~~~   77 (88)
                      ..|+.++..++..  +|.|+|.+  |..+.|.+.+||+|||++|++|+|.. +.+.-+.+|.++++|++|..|...
T Consensus        11 v~Pin~Ifr~Lq~~t~VqIWl~eq~~~rieG~IvGFDEyMNvVlD~aeev~~k~~~rk~lGRilLKGDnItli~~~   86 (88)
T KOG1774|consen   11 VQPINLIFRFLQNRTRVQIWLFEQVGLRIEGRIVGFDEYMNLVLDDAEEVHSKTKSRKELGRILLKGDNITLIQSA   86 (88)
T ss_pred             cCcHHHHHHHHhcCCceEEEEEeccCcEEeEEEechHHhhhhhhcchhhccccccCCCccccEEEcCCcEEEEeec
Confidence            4688888888764  58888876  78999999999999999999999874 232334899999999999999754

>KOG1782|consensus

Probab=99.28  E-value=8.3e-13  Score=86.38  Aligned_cols=72  Identities=26%  Similarity=0.337  Sum_probs=62.2

Q ss_pred             HHHhhcCCCEEEEEEcCccEEEEEEEEecCCcceEEcceEEEe-cCe--eeeeeceEEEeCCcEEEEEcCCCCCc
Q psy6372          11 PFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEII-DGH--CTGKLGEVLIRCNNILYIRGAEEGDE   82 (88)
Q Consensus        11 ~~L~~~i~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~d~~e~~-~~~--~~~~~~~v~IrG~~I~~I~~~d~~~~   82 (88)
                      .-|.+++++++.|-|+|||.+.|.|.|||+|.|++|.+|.|.. -++  .....|.++|||.||+.+...|.+-|
T Consensus        12 ~sl~~~~dkKllVlLRDGR~L~G~LRSfDQFaNlvL~~~iERi~v~~~Y~di~~glfiIRGENVvllGeid~dkE   86 (129)
T KOG1782|consen   12 TSLVEYLDKKLLVLLRDGRKLIGVLRSFDQFANLVLQGVIERIFVGNKYCDIPRGLFIIRGENVVLLGEIDLDKE   86 (129)
T ss_pred             hHHHHHhcceEEEEEecCcchhhhhhhHHHHHHHHHHhhhhheeecceecccCceEEEEecCcEEEEecCCcchh
Confidence            3488899999999999999999999999999999999999863 121  34566899999999999988887777

>KOG3168|consensus

Probab=99.26  E-value=8.1e-13  Score=90.49  Aligned_cols=67  Identities=27%  Similarity=0.288  Sum_probs=59.4

Q ss_pred             HHHhhcCCCEEEEEEcCccEEEEEEEEecCCcceEEcceEEEe----------cCeeeeeeceEEEeCCcEEEEEcC
Q psy6372          11 PFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEII----------DGHCTGKLGEVLIRCNNILYIRGA   77 (88)
Q Consensus        11 ~~L~~~i~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~d~~e~~----------~~~~~~~~~~v~IrG~~I~~I~~~   77 (88)
                      +-|-++++.+++|.++||++|.|++.+||.|||++|.+|.|.+          ++.+.+-+++|++||++|++....
T Consensus         7 skml~~iNyr~rv~~qDgr~~ig~~~afDkhmNlvl~dceE~r~~k~k~~~~~~~eEkr~lgLvllRgenIvs~tVe   83 (177)
T KOG3168|consen    7 SKMLQHINYRMRVRLQDGRTFIGQFKAFDKHMNLVLQDCEEFRKIKPKNRKMTDGEEKRVLGLVLLRGENIVSMTVE   83 (177)
T ss_pred             hHHHHhhcceEEEEeccCceeechhhhhHHHHHHHHHHHHHHhccccccccccccceeeEEEEEEecCCcEEEEecc
Confidence            4567789999999999999999999999999999999999853          244789999999999999998753

>KOG3459|consensus

Probab=98.76  E-value=9.7e-10  Score=70.81  Aligned_cols=69  Identities=14%  Similarity=0.230  Sum_probs=59.3

Q ss_pred             CCcHHHHhhcC--CCEEEEEEcCccEEEEEEEEecCCcceEEcceEEEe-------cCe------eeeeeceEEEeCCcE
Q psy6372           7 CNPKPFLNLLT--GKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEII-------DGH------CTGKLGEVLIRCNNI   71 (88)
Q Consensus         7 ~~p~~~L~~~i--~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~d~~e~~-------~~~------~~~~~~~v~IrG~~I   71 (88)
                      ..|++++.+..  ..+|.|-++|++..-|.+.+||.|.|++|+|+.+.+       +|.      ..++++.+||||++|
T Consensus        23 ~Gpls~~~~~~~~~~~vLi~cRnn~k~l~Rv~afdrhcnmvlenvkelwte~~ks~kgkk~~~~~~~r~isK~flRGdsv  102 (114)
T KOG3459|consen   23 TGPLSVLPASVKNNTQVLINCRNNVKLLGRVKAFDRHCNMVLENVKELWTEVPKSGKGKKAKPVNKDRFISKMFLRGDSV  102 (114)
T ss_pred             cCchhhhHHHhhcCceeEEEecccHHHHhhhhhhhccccchhhcHHHHCCccccCCCcccCCccchhhhhheeeecCCeE
Confidence            47888888886  578999999999999999999999999999999854       122      267899999999999


Q ss_pred             EEEE
Q psy6372          72 LYIR   75 (88)
Q Consensus        72 ~~I~   75 (88)
                      +.+.
T Consensus       103 I~v~  106 (114)
T KOG3459|consen  103 ILVL  106 (114)
T ss_pred             EEEE
Confidence            8875

>PF14438 SM-ATX: Ataxin 2 SM domain; PDB: 1M5Q_1

Probab=98.31  E-value=2.1e-06  Score=51.71  Aligned_cols=63  Identities=19%  Similarity=0.309  Sum_probs=41.7

Q ss_pred             HHHHhhcCCCEEEEEEcCccEEEEEEEEecC---CcceEEcceEEEecC----e---eeeeeceEEEeCCcEE
Q psy6372          10 KPFLNLLTGKSVICKLKWGHEYKGILVSTDG---YMNCQLASTEEIIDG----H---CTGKLGEVLIRCNNIL   72 (88)
Q Consensus        10 ~~~L~~~i~k~V~V~L~~g~~~~G~L~~~D~---~mNlvL~d~~e~~~~----~---~~~~~~~v~IrG~~I~   72 (88)
                      .-++..++|++|.|+++||..|.|.|.+++.   .+.++|+.+......    .   .....+.++|+++.|+
T Consensus         4 ~~l~~~lvG~~V~V~~~~G~~yeGif~s~s~~~~~~~vvLk~a~~~~~~~~~~~~~~~~~~~~tlii~~~dvv   76 (77)
T PF14438_consen    4 VYLLTNLVGQTVEVTTKNGSVYEGIFHSASPESNEFDVVLKMARKVPKSDQSNSDPLSSEIVETLIIPAKDVV   76 (77)
T ss_dssp             HHHHHTTTTSEEEEEETTS-EEEEEEEEE-T---T--EEEEEEEETTS------EEEEEEE-GGGEEE-----
T ss_pred             HHHHHhCcCCEEEEEECCCCEEEEEEEeCCCcccceeEEEEeeeeccccccccCCccCCCCCceEEEeccccC
Confidence            3467889999999999999999999999998   899999988875322    1   2345566777776654

>cd01739 LSm11_C The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation

Probab=98.18  E-value=1.9e-06  Score=51.07  Aligned_cols=36  Identities=22%  Similarity=0.236  Sum_probs=30.8

Q ss_pred             CCEEEEEEcCc----cEEEEEEEEecCCcceEEcceEEEe
Q psy6372          18 GKSVICKLKWG----HEYKGILVSTDGYMNCQLASTEEII   53 (88)
Q Consensus        18 ~k~V~V~L~~g----~~~~G~L~~~D~~mNlvL~d~~e~~   53 (88)
                      +++|+|.++.-    -.++|.|.+||+|||++|.|+.|..
T Consensus         8 r~RVrV~iR~~~gvrG~~~G~lvAFDK~wNm~L~DV~E~y   47 (66)
T cd01739           8 RIRVRVHIRTFKGLRGVCSGFLVAFDKFWNMALVDVDETY   47 (66)
T ss_pred             CcEEEEEEecccCcccEEEEEEEeeeeehhheehhhhhhh
Confidence            57888888763    4788999999999999999999874

Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. LSm11 is an SmD2 - like subunit which binds U7 snRNA along with LSm10 and five other Sm subunits to form a 7-member ring structure. LSm11 and the U7 snRNP of which it is a part are thought to play an important role in histone mRNA 3' processing.

>PF12701 LSM14: Scd6-like Sm domain; PDB: 2RM4_A 2FB7_A 2VC8_A 2VXF_A 2VXE_A

Probab=97.61  E-value=0.00053  Score=43.44  Aligned_cols=68  Identities=19%  Similarity=0.228  Sum_probs=54.3

Q ss_pred             hhcCCCEEEEEEcCccEEEEEEEEecC-CcceEEcceEEE-ecCe--------eeeeeceEEEeCCcEEEEEcCCCCC
Q psy6372          14 NLLTGKSVICKLKWGHEYKGILVSTDG-YMNCQLASTEEI-IDGH--------CTGKLGEVLIRCNNILYIRGAEEGD   81 (88)
Q Consensus        14 ~~~i~k~V~V~L~~g~~~~G~L~~~D~-~mNlvL~d~~e~-~~~~--------~~~~~~~v~IrG~~I~~I~~~d~~~   81 (88)
                      ..++|++|.+..+++-.|.|+|..+|. ...+.|.|+..+ .++.        ....++.+..||+.|.-+.+.+...
T Consensus         4 ~~~IGs~ISlisk~~iRYeG~L~~Id~~~sTItL~nVr~~GtE~R~~~~~ipp~~~v~~~I~Fr~sDIkdL~v~e~~~   81 (96)
T PF12701_consen    4 DPYIGSKISLISKSDIRYEGILYSIDTEDSTITLKNVRSFGTEGRPTDREIPPSDEVYDYIVFRGSDIKDLKVIEPPP   81 (96)
T ss_dssp             CCCTTCEEEEEETTTEEEEEEEEEEETTTTEEEEEEEEETTETTSS-SS---C-CSSSSEEEEETTTEEEEEECE-S-
T ss_pred             ccccCCEEEEEECCCcEEEEEEEEEcCCCCEEEeeeeeecCcCCCCcCcccCCCCceeeEEEEEccccceEEEEcCCC
Confidence            368999999999999999999999995 789999999865 2221        2346789999999999987765443

>PF02237 BPL_C: Biotin protein ligase C terminal domain; InterPro: IPR003142 This C-terminal domain has an SH3-like barrel fold, the function of which is unknown

Probab=97.05  E-value=0.0046  Score=34.06  Aligned_cols=35  Identities=17%  Similarity=0.119  Sum_probs=29.9

Q ss_pred             cCCCEEEEEEcCccEEEEEEEEecCCcceEEcceEE
Q psy6372          16 LTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEE   51 (88)
Q Consensus        16 ~i~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~d~~e   51 (88)
                      .+|++|++.+ ++..++|+..++|++-.|+++....
T Consensus         1 ~lG~~V~v~~-~~~~~~G~~~gId~~G~L~v~~~~g   35 (48)
T PF02237_consen    1 TLGQEVRVET-GDGEIEGIAEGIDDDGALLVRTEDG   35 (48)
T ss_dssp             STTSEEEEEE-TSCEEEEEEEEEETTSEEEEEETTE
T ss_pred             CCCCEEEEEE-CCeEEEEEEEEECCCCEEEEEECCC
Confidence            3799999999 6777799999999999999875543

It is found associated with prokaryotic bifunctional transcriptional repressors [] and eukaryotic enzymes involved in biotin utilization [, ]. In Escherichia coli the biotin operon repressor (BirA) is a bifunctional protein. BirA acts both as the acetyl-coA carboxylase biotin holoenzyme synthetase (6.3.4.15 from EC) and as the biotin operon repressor. DNA sequence analysis of mutations indicates that the helix-turn-helix DNA binding region is located at the N terminus while mutations affecting enzyme function, although mapping over a large region, are found mainly in the central part of the protein's primary sequence [].; GO: 0006464 protein modification process; PDB: 3RUX_A 2CGH_A 3L1A_B 3L2Z_A 1HXD_A 1BIB_A 2EWN_B 1BIA_A 2EJ9_A 3FJP_A ....

>PF06372 Gemin6: Gemin6 protein; InterPro: IPR009422 This family consists of several mammalian Gemin6 proteins

Probab=96.89  E-value=0.0025  Score=44.07  Aligned_cols=68  Identities=26%  Similarity=0.302  Sum_probs=45.7

Q ss_pred             CCCcHHHHhhcCCCEEEEEEcCccEEEEEEEEecC-CcceEEcceEEEecCeeeeeeceEEEeCCcEEEEEcCCCCC
Q psy6372           6 PCNPKPFLNLLTGKSVICKLKWGHEYKGILVSTDG-YMNCQLASTEEIIDGHCTGKLGEVLIRCNNILYIRGAEEGD   81 (88)
Q Consensus         6 ~~~p~~~L~~~i~k~V~V~L~~g~~~~G~L~~~D~-~mNlvL~d~~e~~~~~~~~~~~~v~IrG~~I~~I~~~d~~~   81 (88)
                      ...|+. +..|++|.|.|.+.| +++.|-|..+|+ .-|++|-+..+  +++  .  .--+|.|..|..|...++.+
T Consensus         6 ~~~p~~-~~~yv~K~VkV~~~d-~~~~G~v~TiDPVS~siVL~~~~e--~~~--~--sv~~I~ghaVk~vevl~~~~   74 (166)
T PF06372_consen    6 KKSPLE-WQDYVGKEVKVTLSD-KEYKGWVYTIDPVSASIVLVNFQE--DGK--R--SVKVIMGHAVKSVEVLSEGD   74 (166)
T ss_dssp             HS-HHH-HHCTTT-EEEEEETT-EEEEEEEEEE-TTT--EEEEEE-T--TS---E--EEEEE-GGGEEEEEEEE---
T ss_pred             hCCHHH-HHHhhCcEEEEEEec-cEEEEEEEEeCCCCCeEEEEEccc--CCc--e--eEEEEEccceEEEEEccCCc
Confidence            345554 468999999999999 999999999995 68899886664  222  2  24689999999998877643

The exact function of Gemin6 is unknown but it has been found to form part of the Survival of motor neuron complex. The SMN complex plays a key role in the biogenesis of spliceosomal small nuclear ribonucleoproteins (snRNPs) and other ribonucleoprotein particles [].; GO: 0000245 spliceosome assembly, 0005634 nucleus; PDB: 1Y96_A.

>cd01736 LSm14_N LSm14 (also known as RAP55) belongs to a family of Sm-like proteins that associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation

Probab=96.81  E-value=0.0095  Score=36.16  Aligned_cols=59  Identities=17%  Similarity=0.229  Sum_probs=46.5

Q ss_pred             hhcCCCEEEEEEcCccEEEEEEEEec-CCcceEEcceEEE-ecC-----e----eeeeeceEEEeCCcEE
Q psy6372          14 NLLTGKSVICKLKWGHEYKGILVSTD-GYMNCQLASTEEI-IDG-----H----CTGKLGEVLIRCNNIL   72 (88)
Q Consensus        14 ~~~i~k~V~V~L~~g~~~~G~L~~~D-~~mNlvL~d~~e~-~~~-----~----~~~~~~~v~IrG~~I~   72 (88)
                      ..++|+++.+..+.+-.|.|+|.++| +..-+.|.|+..+ .+|     .    ...-++.+..||+.|.
T Consensus         2 ~~~IG~~isLISk~~iRYeGiL~~In~~~sTi~L~nVr~fGTEgR~~~~~~ipp~~~vyd~IvFrgsDIk   71 (74)
T cd01736           2 TPYIGSKISLISKSDIRYEGILYTINTEDSTIALKNVRSFGTEGRPTDGPEIPPSDEVYDYIVFRGSDIK   71 (74)
T ss_pred             ccccCceEEEEecCCcEEEEEEEeeccccCEEEeeeeEeecccCCCCCCCccCCCCcceeEEEEcCCccc
Confidence            36899999999999999999999999 4577889998865 221     1    3445678888988775

Members of this family share a highly conserved Sm fold, containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet, that associates with other Sm proteins to form hexameric and heptameric ring structures. In addition to the N-terminal Sm-like domain, LSm14 has an uncharacterized C-terminal domain containing a conserved DFDF box. In Xenopus laevis, LSm14 is an oocyte-specific constituent of ribonucleoprotein particles.

>PF11095 Gemin7: Gem-associated protein 7 (Gemin7); InterPro: IPR020338 Gem-associated protein 7 (Gemin7) is a component of the survival of motor neuron complex, which functions in the assembly of spliceosomal small nuclear ribonucleoproteins

Probab=96.72  E-value=0.014  Score=35.95  Aligned_cols=63  Identities=22%  Similarity=0.202  Sum_probs=46.8

Q ss_pred             HHHHhhcCCCEEEEEEcCccEEEEEEEEecC-CcceEEcceEEEecCeeeeeeceEEEeCCcEEEEEcC
Q psy6372          10 KPFLNLLTGKSVICKLKWGHEYKGILVSTDG-YMNCQLASTEEIIDGHCTGKLGEVLIRCNNILYIRGA   77 (88)
Q Consensus        10 ~~~L~~~i~k~V~V~L~~g~~~~G~L~~~D~-~mNlvL~d~~e~~~~~~~~~~~~v~IrG~~I~~I~~~   77 (88)
                      +.+|..+.|++|.+.|.++.+..|++.++|. ..|+..+|-+ ++=|    ..+.-.+|..-|.++...
T Consensus        16 Lr~l~~~~gk~v~f~l~e~t~V~a~F~a~d~~~~~f~Vs~L~-TPlG----v~~eAlLR~~DVi~~~f~   79 (80)
T PF11095_consen   16 LRSLLAMVGKPVEFTLHENTTVSARFGACDIDVSNFQVSNLQ-TPLG----VQPEALLRCSDVISISFD   79 (80)
T ss_dssp             HHHHHHCTTSEEEEEEGGG-EEEEEEEEE-TTS-EEEEEEEE-TTTT----EEEEEEEEGGGEEEEEE-
T ss_pred             HHHHHHhcCCceEEEEeCCeEEEEEEEEecCchheEEhhhcC-CCcc----cChhheeecCCEEEEEec
Confidence            5678889999999999999999999999994 5777666554 2223    246789999999998754

Gemin7 interacts with several Sm proteins of spliceosomal small nuclear ribonucleoproteins, especially SmE []. Gem-associated protein 7 is found in the nucleoplasm, in nuclear "gems" (Gemini of Cajal bodies), and in the cytoplasm. Three transcript variants encoding the same protein have been found for this gene [].; GO: 0032797 SMN complex; PDB: 1Y96_D.

>PF10842 DUF2642: Protein of unknown function (DUF2642); InterPro: IPR020139 This entry contains proteins with no known function

Probab=96.51  E-value=0.022  Score=33.80  Aligned_cols=54  Identities=26%  Similarity=0.384  Sum_probs=41.0

Q ss_pred             HHHHhhcCCCEEEEEEcCccEEEEEEEEecCCcceEEcceEEEecCeeeeeeceEEEeCCcEEEEEc
Q psy6372          10 KPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTGKLGEVLIRCNNILYIRG   76 (88)
Q Consensus        10 ~~~L~~~i~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~d~~e~~~~~~~~~~~~v~IrG~~I~~I~~   76 (88)
                      .+.|++++|++|.|++-.|+. +|+|.++-+.- ++|+..     +      ..+|||=.+|++|.+
T Consensus        13 yq~lq~liG~~vvV~T~~g~v-~G~L~~V~pDh-Ivl~~~-----~------~~~~IR~~~IV~v~p   66 (66)
T PF10842_consen   13 YQTLQSLIGQRVVVQTTRGSV-RGILVDVKPDH-IVLEEN-----G------TPFFIRIAQIVWVMP   66 (66)
T ss_pred             HHHHHHhcCCEEEEEEcCCcE-EEEEEeecCCE-EEEEeC-----C------cEEEEEeeeEEEEcC
Confidence            468999999999999987766 99999998543 343322     2      367899889988853

>cd01716 Hfq Hfq, an abundant, ubiquitous RNA-binding protein, functions as a pleiotrophic regulator of RNA metabolism in prokaryotes, required for transcription of some transcripts and degradation of others

Probab=96.30  E-value=0.014  Score=34.16  Aligned_cols=34  Identities=29%  Similarity=0.267  Sum_probs=28.3

Q ss_pred             HHhhcC--CCEEEEEEcCccEEEEEEEEecCCcceE
Q psy6372          12 FLNLLT--GKSVICKLKWGHEYKGILVSTDGYMNCQ   45 (88)
Q Consensus        12 ~L~~~i--~k~V~V~L~~g~~~~G~L~~~D~~mNlv   45 (88)
                      ||+.+.  ..+|+|-|.||-.++|.+.+||+|+=+.
T Consensus         3 fln~~r~~~~~Vtv~L~NG~~l~G~I~~fD~ftVll   38 (61)
T cd01716           3 FLNAARKEKIPVTIYLVNGVQLKGQIESFDNFTVLL   38 (61)
T ss_pred             HHHHHHHcCCcEEEEEeCCcEEEEEEEEEcceEEEE
Confidence            555554  5679999999999999999999998444

Hfq binds small RNA molecules called riboregulators that modulate the stability or translation efficiency of RNA transcripts. Hfq binds preferentially to unstructured A/U-rich RNA sequences and is similar to the eukaryotic Sm proteins in both sequence and structure. Hfq forms a homo-hexameric ring similar to the heptameric ring of the Sm proteins.

>cd01735 LSm12_N LSm12 belongs to a family of Sm-like proteins that associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation

Probab=96.17  E-value=0.019  Score=33.61  Aligned_cols=35  Identities=17%  Similarity=0.245  Sum_probs=29.8

Q ss_pred             cCCCEEEEEEcCccEEEEEEEEecCCcceEEcceE
Q psy6372          16 LTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTE   50 (88)
Q Consensus        16 ~i~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~d~~   50 (88)
                      .+|.+|++++..|..++|.+.+||...++.+-.+.
T Consensus         4 ~iGs~V~~kTc~g~~ieGEV~afD~~tk~lIlk~~   38 (61)
T cd01735           4 SVGSQVSCRTCFEQRLQGEVVAFDYPSKMLILKCP   38 (61)
T ss_pred             ccccEEEEEecCCceEEEEEEEecCCCcEEEEECc
Confidence            47999999999999999999999988777654433

Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet that associates with other Sm proteins to form hexameric and heptameric ring structures. In addition to the N-terminal Sm-like domain, LSm12 has a novel methyltransferase domain.

>PRK14638 hypothetical protein; Provisional

Probab=96.16  E-value=0.017  Score=39.09  Aligned_cols=45  Identities=22%  Similarity=0.102  Sum_probs=36.0

Q ss_pred             CCCCCCCcH---HHHhhcCCCEEEEEEcCccEEEEEEEEecCCcceEEc
Q psy6372           2 STPLPCNPK---PFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLA   47 (88)
Q Consensus         2 ~~~~~~~p~---~~L~~~i~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~   47 (88)
                      ||+...-|+   .-+..++|++|.|++.+++.++|+|.++|+. ++.|.
T Consensus        81 SSPGldRpL~~~~~f~r~~G~~v~V~~~~~k~~~G~L~~~~~~-~i~l~  128 (150)
T PRK14638         81 SSPGLDRPLRGPKDYVRFTGKLAKIVTKDGKTFIGRIESFVDG-TITIS  128 (150)
T ss_pred             eCCCCCCCCCCHHHHHHhCCCEEEEEECCCcEEEEEEEEEeCC-EEEEE
Confidence            666666665   4566789999999999999999999999974 35554

>TIGR02383 Hfq RNA chaperone Hfq

Probab=95.86  E-value=0.022  Score=33.34  Aligned_cols=35  Identities=31%  Similarity=0.354  Sum_probs=28.8

Q ss_pred             HHHhhcC--CCEEEEEEcCccEEEEEEEEecCCcceE
Q psy6372          11 PFLNLLT--GKSVICKLKWGHEYKGILVSTDGYMNCQ   45 (88)
Q Consensus        11 ~~L~~~i--~k~V~V~L~~g~~~~G~L~~~D~~mNlv   45 (88)
                      .||..+.  +.+|+|-|.||-.++|.+.+||+|+=+.
T Consensus         6 ~fln~~r~~~~~Vti~L~nG~~l~G~I~~fD~ftVll   42 (61)
T TIGR02383         6 QFLNTLRKERIPVTVFLVNGVQLKGVIESFDNFTVLL   42 (61)
T ss_pred             HHHHHHHHcCCcEEEEEeCCcEEEEEEEEEeeeEEEE
Confidence            3565553  5779999999999999999999998444

This model represents the RNA-binding pleiotropic regulator Hfq, a small, Sm-like protein of bacteria. It helps pair regulatory noncoding RNAs with complementary mRNA target regions. It enhances the elongation of poly(A) tails on mRNA. It appears also to protect RNase E recognition sites (A/U-rich sequences with adjacent stem-loop structures) from cleavage. Being pleiotropic, it differs in some of its activities in different species. Hfq binds the non-coding regulatory RNA DsrA (see Rfam RF00014) in the few species known to have it: Escherichia coli, Shigella flexneri, Salmonella spp. In Azorhizobium caulinodans, an hfq mutant is unable to express nifA, and Hfq is called NrfA, for nif regulatory factor (see PubMed:8197116). The name hfq reflects phenomenology as a host factor for phage Q-beta RNA replication.

>PRK14639 hypothetical protein; Provisional

Probab=95.82  E-value=0.03  Score=37.43  Aligned_cols=44  Identities=23%  Similarity=0.193  Sum_probs=35.7

Q ss_pred             CCCCCCCcH---HHHhhcCCCEEEEEEcCccEEEEEEEEecCCcceEE
Q psy6372           2 STPLPCNPK---PFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQL   46 (88)
Q Consensus         2 ~~~~~~~p~---~~L~~~i~k~V~V~L~~g~~~~G~L~~~D~~mNlvL   46 (88)
                      ||+...-|+   .-+..++|+.|.|++.+++.+.|+|.++|+. ++.|
T Consensus        69 SSPGl~RpL~~~~~f~r~~G~~v~v~l~~~~~~~G~L~~~~~~-~i~l  115 (140)
T PRK14639         69 SSPGLERKLSKIEHFAKSIGELVKITTNEKEKFEGKIVSVDDE-NITL  115 (140)
T ss_pred             eCCCCCCcCCCHHHHHHhCCCEEEEEECCCcEEEEEEEEEeCC-EEEE
Confidence            566666665   4567889999999999999999999999984 4555

>COG1923 Hfq Uncharacterized host factor I protein [General function prediction only]

Probab=95.74  E-value=0.032  Score=34.04  Aligned_cols=38  Identities=34%  Similarity=0.443  Sum_probs=30.4

Q ss_pred             HHHhhc--CCCEEEEEEcCccEEEEEEEEecCCcceEEcce
Q psy6372          11 PFLNLL--TGKSVICKLKWGHEYKGILVSTDGYMNCQLAST   49 (88)
Q Consensus        11 ~~L~~~--i~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~d~   49 (88)
                      .||.++  -+.+|.|-|.||-..+|.+.+||+|. +.|++.
T Consensus        10 ~fLn~~Rk~~i~VtIfLvNG~~L~G~V~sfD~f~-VlL~~~   49 (77)
T COG1923          10 PFLNALRKEKIPVTIFLVNGFKLQGQVESFDNFV-VLLKNT   49 (77)
T ss_pred             HHHHHHHhcCCeEEEEEEcCEEEEEEEEeeeeEE-EEEEcC
Confidence            466655  46789999999999999999999997 444443

>PRK02001 hypothetical protein; Validated

Probab=95.62  E-value=0.041  Score=37.42  Aligned_cols=45  Identities=20%  Similarity=0.177  Sum_probs=36.1

Q ss_pred             CCCCCCCcHH---HHhhcCCCEEEEEEcCccEEEEEEEEecCCcceEEc
Q psy6372           2 STPLPCNPKP---FLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLA   47 (88)
Q Consensus         2 ~~~~~~~p~~---~L~~~i~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~   47 (88)
                      ||+.-.-|+.   -+..++|+.|.|++.+++.+.|+|.++|+. ++.|.
T Consensus        71 SSPGldRpL~~~~~f~r~~G~~v~V~l~~~~~~~G~L~~~~~~-~i~l~  118 (152)
T PRK02001         71 GSAGLTSPLKVPRQYKKNIGRELEVLTKNGKKIEGELKSADEN-DITLE  118 (152)
T ss_pred             eCCCCCCcCCCHHHHHHhCCCEEEEEECCCCEEEEEEEEEeCC-EEEEE
Confidence            6666666654   556779999999999999999999999975 35553

>PRK00395 hfq RNA-binding protein Hfq; Provisional

Probab=95.53  E-value=0.032  Score=34.26  Aligned_cols=39  Identities=28%  Similarity=0.341  Sum_probs=31.3

Q ss_pred             HHHHhhcC--CCEEEEEEcCccEEEEEEEEecCCcceEEcc
Q psy6372          10 KPFLNLLT--GKSVICKLKWGHEYKGILVSTDGYMNCQLAS   48 (88)
Q Consensus        10 ~~~L~~~i--~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~d   48 (88)
                      -.||..+.  +.+|+|-|.||-.++|.+.+||+|.=+.-.+
T Consensus         9 d~fLn~lr~~~~~VtifL~NG~~l~G~I~~fD~ftVll~~~   49 (79)
T PRK00395          9 DPFLNALRKERVPVTIYLVNGIKLQGQIESFDNFVVLLRNT   49 (79)
T ss_pred             HHHHHHHHHcCCCEEEEEeCCcEEEEEEEEEccEEEEEEEC
Confidence            35666664  6779999999999999999999998555434

>PRK14644 hypothetical protein; Provisional

Probab=95.25  E-value=0.047  Score=36.41  Aligned_cols=45  Identities=18%  Similarity=0.025  Sum_probs=35.6

Q ss_pred             CCCCCCCcHH--HHhhcCCCEEEEEEcCc----cEEEEEEEEecCCcceEEc
Q psy6372           2 STPLPCNPKP--FLNLLTGKSVICKLKWG----HEYKGILVSTDGYMNCQLA   47 (88)
Q Consensus         2 ~~~~~~~p~~--~L~~~i~k~V~V~L~~g----~~~~G~L~~~D~~mNlvL~   47 (88)
                      ||+.-.-|+.  -+..++|+.|.|+|++.    +.+.|+|.++|+. ++.|.
T Consensus        67 SSPGldRpL~~~~f~r~~G~~v~V~l~~~~~~~~~~~G~L~~v~~~-~i~l~  117 (136)
T PRK14644         67 SSPGFDMDYETDELENHIGEIIDVSLNKEVNKTDFITGELLENNPE-TITLK  117 (136)
T ss_pred             ECCCCCCCCCHHHHHHhCCCeEEEEEccCcCCeEEEEEEEEEEeCC-EEEEE
Confidence            5666666654  47788999999999887    9999999999974 46554

>PRK14640 hypothetical protein; Provisional

Probab=94.52  E-value=0.12  Score=34.88  Aligned_cols=45  Identities=20%  Similarity=0.310  Sum_probs=34.8

Q ss_pred             CCCCCCCcH---HHHhhcCCCEEEEEE----cCccEEEEEEEEecCCcceEEc
Q psy6372           2 STPLPCNPK---PFLNLLTGKSVICKL----KWGHEYKGILVSTDGYMNCQLA   47 (88)
Q Consensus         2 ~~~~~~~p~---~~L~~~i~k~V~V~L----~~g~~~~G~L~~~D~~mNlvL~   47 (88)
                      ||+...-|+   .-+.+++|+.|.|+|    .+.+.++|+|.++|+. ++.|.
T Consensus        78 SSPGl~RpL~~~~~f~r~~G~~v~V~l~~~~~~~k~~~G~L~~v~~~-~v~l~  129 (152)
T PRK14640         78 SSPGLDRPLFKVAQFEKYVGQEAAVTLRMATNNRRKFKGVIKAVQGD-MITLT  129 (152)
T ss_pred             eCCCCCCcCCCHHHHHHhCCCeEEEEEecccCCceEEEEEEEEEeCC-EEEEE
Confidence            666666665   456678999999999    5679999999999975 35553

>COG0779 Uncharacterized protein conserved in bacteria [Function unknown]

Probab=94.50  E-value=0.17  Score=34.48  Aligned_cols=44  Identities=27%  Similarity=0.395  Sum_probs=35.9

Q ss_pred             CCCCCCCcH---HHHhhcCCCEEEEEE----cCccEEEEEEEEecCCcceEE
Q psy6372           2 STPLPCNPK---PFLNLLTGKSVICKL----KWGHEYKGILVSTDGYMNCQL   46 (88)
Q Consensus         2 ~~~~~~~p~---~~L~~~i~k~V~V~L----~~g~~~~G~L~~~D~~mNlvL   46 (88)
                      ||+...-|+   .-+..++|+.|.|+|    .+.+.+.|+|.++|+.. +++
T Consensus        80 SSPGldRpL~~~~~f~r~~G~~Vkv~l~~~~~~~k~~~G~i~~~d~~~-v~~  130 (153)
T COG0779          80 SSPGLDRPLKTAEHFARFIGEKVKVKLRLPIEGRKKFEGKIVAVDGET-VTL  130 (153)
T ss_pred             eCCCCCCCcCCHHHHHHhcCcEEEEEEecccCCceEEEEEEEEEcCCe-EEE
Confidence            666666665   466777999999999    78899999999999887 444

>cd01734 YlxS_C YxlS is a Bacillus subtilis gene of unknown function with two domains that each have an alpha/beta fold

Probab=94.49  E-value=0.16  Score=30.74  Aligned_cols=44  Identities=32%  Similarity=0.381  Sum_probs=33.8

Q ss_pred             CCCCCCCcH---HHHhhcCCCEEEEEEc---Cc-cEEEEEEEEecCCcceEE
Q psy6372           2 STPLPCNPK---PFLNLLTGKSVICKLK---WG-HEYKGILVSTDGYMNCQL   46 (88)
Q Consensus         2 ~~~~~~~p~---~~L~~~i~k~V~V~L~---~g-~~~~G~L~~~D~~mNlvL   46 (88)
                      ||+...-|+   .-+..++|+.|.|+++   +| +.+.|.|.++|+. ++.|
T Consensus         6 SSPGl~RpL~~~~~~~r~~G~~v~v~~~~~~~~~~~~~G~L~~~~~~-~v~l   56 (83)
T cd01734           6 SSPGAERPLKKEADFERAVGKYVHVKLYQPIDGQKEFEGTLLGVDDD-TVTL   56 (83)
T ss_pred             cCCCCCCcCCCHHHHHHhCCCEEEEEEEcccCCeEEEEEEEEeEeCC-EEEE
Confidence            666666665   4566779999999997   55 6899999999985 3444

The N-terminal domain is composed of two alpha-helices and a three-stranded beta-sheet, while the C-terminal domain is composed of one alpha-helix and a five-stranded beta-sheet. This CD represents the C-terminal domain which has a fold similar to the Sm fold of proteins like Sm-D3.

>PRK14091 RNA-binding protein Hfq; Provisional

Probab=94.49  E-value=0.12  Score=35.66  Aligned_cols=48  Identities=23%  Similarity=0.194  Sum_probs=35.0

Q ss_pred             CCCCCCCCcHHHHhhcC--CCEEEEEEcCccEEEEEEEEecCCcceEEcc
Q psy6372           1 MSTPLPCNPKPFLNLLT--GKSVICKLKWGHEYKGILVSTDGYMNCQLAS   48 (88)
Q Consensus         1 m~~~~~~~p~~~L~~~i--~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~d   48 (88)
                      |++.....--.||..+.  ..+|+|-|.||-.++|++.+||+|.=+.-.+
T Consensus         5 m~~~~~nlQD~fLn~~Rk~k~~VtvfL~nG~rl~G~I~~fD~ftVlL~~~   54 (165)
T PRK14091          5 MAEKVNNLQDIFLNSLRKTKTPVTMFLVKGVKLQGIITWFDNFSILLRRD   54 (165)
T ss_pred             ccccccchHHHHHHHHHhcCCcEEEEEecCcEEEEEEEEEcceEEEEEeC
Confidence            44333333356788775  4568999999999999999999998444434

>PF02576 DUF150: Uncharacterised BCR, YhbC family COG0779; InterPro: IPR003728 The RimP protein facilitates maturation of the 30S ribsomal subunit, and is required for the efficient production of translationally competent ribosmomes []

Probab=94.23  E-value=0.098  Score=34.57  Aligned_cols=44  Identities=30%  Similarity=0.345  Sum_probs=29.4

Q ss_pred             CCCCCCCcH---HHHhhcCCCEEEEEEc----CccEEEEEEEEecCCcceEE
Q psy6372           2 STPLPCNPK---PFLNLLTGKSVICKLK----WGHEYKGILVSTDGYMNCQL   46 (88)
Q Consensus         2 ~~~~~~~p~---~~L~~~i~k~V~V~L~----~g~~~~G~L~~~D~~mNlvL   46 (88)
                      ||+...-|+   .-+..++|+.|.|+++    +.+.+.|+|.++|+ -.++|
T Consensus        68 SSPG~~r~L~~~~~~~~~iG~~v~v~~~~~~~~~~~~~G~L~~~~~-~~i~l  118 (141)
T PF02576_consen   68 SSPGIDRPLKSPRDFERFIGRKVKVKLKQPVNGRKEFEGKLLEVDE-DEITL  118 (141)
T ss_dssp             E--SSSS--SSHHHHHHH-SEEEEEE-SS-SSS-SEEEEEEEEEET-TEEEE
T ss_pred             eCCCCCCcCCCHHHHHHhcCCeEEEEEeccCCCcEEEEEEEEEEeC-CEEEE
Confidence            677767776   4678889999999994    45899999999998 33444

; PDB: 1IB8_A.

>PRK14633 hypothetical protein; Provisional

Probab=94.16  E-value=0.16  Score=34.24  Aligned_cols=45  Identities=24%  Similarity=0.214  Sum_probs=34.6

Q ss_pred             CCCCCCCcH---HHHhhcCCCEEEEEEc----CccEEEEEEEEecCCcceEEc
Q psy6372           2 STPLPCNPK---PFLNLLTGKSVICKLK----WGHEYKGILVSTDGYMNCQLA   47 (88)
Q Consensus         2 ~~~~~~~p~---~~L~~~i~k~V~V~L~----~g~~~~G~L~~~D~~mNlvL~   47 (88)
                      ||+.-.-|+   .-+.+++|++|.|+++    +.+.++|+|.++++. ++.|.
T Consensus        75 SSPGldRpL~~~~~f~r~~G~~v~V~~~~~~~~~~~~~G~L~~v~~~-~i~l~  126 (150)
T PRK14633         75 SSPGMNRQIFNIIQAQALVGFNVKAVTLAPVGSQTKFKGVLERVEGN-NVILN  126 (150)
T ss_pred             eCCCCCCCCCCHHHHHHhCCCeEEEEEecccCCcEEEEEEEEEEeCC-EEEEE
Confidence            666666665   4556779999999993    569999999999885 45553

>PRK14645 hypothetical protein; Provisional

Probab=94.07  E-value=0.15  Score=34.62  Aligned_cols=43  Identities=16%  Similarity=0.313  Sum_probs=33.7

Q ss_pred             CCCCCCCcH---HHHhhcCCCEEEEEEcCccEEEEEEEEecCCcceEE
Q psy6372           2 STPLPCNPK---PFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQL   46 (88)
Q Consensus         2 ~~~~~~~p~---~~L~~~i~k~V~V~L~~g~~~~G~L~~~D~~mNlvL   46 (88)
                      ||+...-|+   .-+.+++|+.|.|++ +++.+.|+|.++|+. .+.|
T Consensus        83 SSPGldRpL~~~~df~r~~G~~v~v~~-~~k~~~G~L~~~~d~-~i~l  128 (154)
T PRK14645         83 ESPGPKRPLFTARHFERFAGLKAKVRG-PGENFTGRIKAVSGD-QVTF  128 (154)
T ss_pred             eCCCCCCCCCCHHHHHHhCCCEEEEEc-CCeEEEEEEEEEeCC-EEEE
Confidence            666666675   455677999999986 789999999999975 3554

>PRK14642 hypothetical protein; Provisional

Probab=93.65  E-value=0.14  Score=36.33  Aligned_cols=44  Identities=20%  Similarity=0.264  Sum_probs=34.7

Q ss_pred             CCCCCCCcHH---HHhhcCCCEEEEEEc-------------CccEEEEEEEEecCCcceEE
Q psy6372           2 STPLPCNPKP---FLNLLTGKSVICKLK-------------WGHEYKGILVSTDGYMNCQL   46 (88)
Q Consensus         2 ~~~~~~~p~~---~L~~~i~k~V~V~L~-------------~g~~~~G~L~~~D~~mNlvL   46 (88)
                      ||+-..-|+.   -+.+++|+.|.|+|+             +.+.++|+|.++|+. ++.|
T Consensus        81 SSPGldRPLk~~~df~rfiG~~V~V~l~~pi~~~~~~~~~~~rk~f~G~L~~~~~~-~i~l  140 (197)
T PRK14642         81 SSPGIDRPLRHEQDFERFAGEVIDITLKAPIGAAAGGQVSANRKKFRGTLERAESG-GWQI  140 (197)
T ss_pred             eCCCCCCCCCCHHHHHHhCCCeEEEEEeccccccccccccCCceEEEEEEEEEcCC-EEEE
Confidence            6666666764   556779999999998             679999999999975 4544

>PRK14643 hypothetical protein; Provisional

Probab=93.56  E-value=0.23  Score=34.07  Aligned_cols=40  Identities=15%  Similarity=0.003  Sum_probs=32.6

Q ss_pred             CCCCCCCcH---HHHhhcCCCEEEEEEcC----ccEEEEEEEEecCC
Q psy6372           2 STPLPCNPK---PFLNLLTGKSVICKLKW----GHEYKGILVSTDGY   41 (88)
Q Consensus         2 ~~~~~~~p~---~~L~~~i~k~V~V~L~~----g~~~~G~L~~~D~~   41 (88)
                      ||+.-.-|+   .-+..++|+.|.|+|++    .+.+.|+|.++|..
T Consensus        85 SSPGleRpL~~~~df~r~~G~~V~V~l~~~~~g~k~~~G~L~~~~~~  131 (164)
T PRK14643         85 SSSGIEKQIRSQEELVKALNQWVYVQLNNEIKKVKEFEGYVTKYNVN  131 (164)
T ss_pred             cCCCCCCCCCCHHHHHHhcCCeEEEEEecccCCceEEEEEEEEEeCC
Confidence            666666665   46678899999999965    59999999999965

>PRK14632 hypothetical protein; Provisional

Probab=93.53  E-value=0.24  Score=34.20  Aligned_cols=45  Identities=20%  Similarity=0.283  Sum_probs=34.8

Q ss_pred             CCCCCCCcH---HHHhhcCCCEEEEEEcC-------ccEEEEEEEEecCCcceEEc
Q psy6372           2 STPLPCNPK---PFLNLLTGKSVICKLKW-------GHEYKGILVSTDGYMNCQLA   47 (88)
Q Consensus         2 ~~~~~~~p~---~~L~~~i~k~V~V~L~~-------g~~~~G~L~~~D~~mNlvL~   47 (88)
                      ||+...-|+   .-+..++|+.|.|+|.+       .+.+.|+|.++|+. ++.|.
T Consensus        79 SSPGldRpL~~~~~f~r~iG~~V~V~l~~~~~~~~g~k~~~G~L~~v~~~-~i~l~  133 (172)
T PRK14632         79 SSPGLERPFFRAEQMSPYVGRQIELTLIDPTPEWPGRRKFRGELLAVEGD-TVVLR  133 (172)
T ss_pred             eCCCCCCcCCCHHHHHHhCCCEEEEEEeccccccCCceEEEEEEEEEeCC-EEEEE
Confidence            666666665   45677899999999975       58999999999874 45554

>PRK14636 hypothetical protein; Provisional

Probab=93.40  E-value=0.24  Score=34.35  Aligned_cols=44  Identities=23%  Similarity=0.277  Sum_probs=33.7

Q ss_pred             CCCCCCCcH---HHHhhcCCCEEEEEEc---Cc-cEEEEEEEEecCCcceEE
Q psy6372           2 STPLPCNPK---PFLNLLTGKSVICKLK---WG-HEYKGILVSTDGYMNCQL   46 (88)
Q Consensus         2 ~~~~~~~p~---~~L~~~i~k~V~V~L~---~g-~~~~G~L~~~D~~mNlvL   46 (88)
                      ||+.-.-|+   .-+..++|+.|.|+|+   +| +.++|+|.++|+. ++.|
T Consensus        79 SSPGldRpL~~~~df~r~~G~~V~V~l~~~~~g~k~~~G~L~~v~~~-~v~l  129 (176)
T PRK14636         79 SSPGIDRPLTRPKDFADWAGHEARIALSEPLDGRKQFRGELKGIDGD-TVTI  129 (176)
T ss_pred             eCCCCCCCCCCHHHHHHhCCCeEEEEEecccCCeEEEEEEEEEEeCC-EEEE
Confidence            566666665   4566789999999997   45 7999999999874 3554

>PRK14091 RNA-binding protein Hfq; Provisional

Probab=93.35  E-value=0.93  Score=31.39  Aligned_cols=39  Identities=21%  Similarity=0.181  Sum_probs=31.1

Q ss_pred             HHHhhcC--CCEEEEEEcCccEEEEEEEEecCCcceEEcce
Q psy6372          11 PFLNLLT--GKSVICKLKWGHEYKGILVSTDGYMNCQLAST   49 (88)
Q Consensus        11 ~~L~~~i--~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~d~   49 (88)
                      .||..+.  ..+|+|-|.||-.++|.+.+||+|.=+.-.+.
T Consensus        95 ~fLn~~rk~k~~VtvfL~NG~~l~G~I~~fD~ftvlL~~~g  135 (165)
T PRK14091         95 VFLSAVRDSGEPVTMFLVNGVMLQGEIAAFDLFCMLLERDG  135 (165)
T ss_pred             HHHHHHHhcCCcEEEEEecCcEEEEEEEEEcceEEEEEeCC
Confidence            4677664  56799999999999999999999985554443

>PRK14634 hypothetical protein; Provisional

Probab=93.32  E-value=0.27  Score=33.39  Aligned_cols=44  Identities=16%  Similarity=0.150  Sum_probs=33.6

Q ss_pred             CCCCCCCcH---HHHhhcCCCEEEEEEcCc----cEEEEEEEEecCCcceEE
Q psy6372           2 STPLPCNPK---PFLNLLTGKSVICKLKWG----HEYKGILVSTDGYMNCQL   46 (88)
Q Consensus         2 ~~~~~~~p~---~~L~~~i~k~V~V~L~~g----~~~~G~L~~~D~~mNlvL   46 (88)
                      ||+...-|+   .-+..++|+.|.|+|.+.    +.+.|+|.++|+.. +.|
T Consensus        81 SSPGldRpL~~~~~f~r~~G~~V~V~l~~~~~~~k~~~G~L~~~~~~~-v~l  131 (155)
T PRK14634         81 SSPGIGDQLSSDRDFQTFRGFPVEVSHRDDDGSEQRLEGLLLERNEDH-LQI  131 (155)
T ss_pred             eCCCCCCcCCCHHHHHHhCCCeEEEEEecCCCCeEEEEEEEEEEeCCE-EEE
Confidence            666666665   456678999999999742    89999999999753 555

>PRK00092 ribosome maturation protein RimP; Reviewed

Probab=93.17  E-value=0.3  Score=32.87  Aligned_cols=40  Identities=30%  Similarity=0.428  Sum_probs=32.4

Q ss_pred             CCCCCCCcH---HHHhhcCCCEEEEEE----cCccEEEEEEEEecCC
Q psy6372           2 STPLPCNPK---PFLNLLTGKSVICKL----KWGHEYKGILVSTDGY   41 (88)
Q Consensus         2 ~~~~~~~p~---~~L~~~i~k~V~V~L----~~g~~~~G~L~~~D~~   41 (88)
                      ||+...-|+   .-+..++|+.|.|++    .+++.+.|+|.++|+.
T Consensus        79 SSPGi~RpL~~~~~f~r~~G~~v~V~~~~~~~~~~~~~G~L~~~~~~  125 (154)
T PRK00092         79 SSPGLDRPLKKARDFRRFIGREVKVKLYEPIDGRKKFQGILLAVDGE  125 (154)
T ss_pred             eCCCCCCcCCCHHHHHHhCCCeEEEEEEcccCCceEEEEEEEEeeCC
Confidence            666666665   457788999999997    5678999999999984

>PRK14646 hypothetical protein; Provisional

Probab=93.04  E-value=0.33  Score=32.96  Aligned_cols=45  Identities=13%  Similarity=0.060  Sum_probs=34.5

Q ss_pred             CCCCCCCcH---HHHhhcCCCEEEEEEcCc----cEEEEEEEEecCCcceEEc
Q psy6372           2 STPLPCNPK---PFLNLLTGKSVICKLKWG----HEYKGILVSTDGYMNCQLA   47 (88)
Q Consensus         2 ~~~~~~~p~---~~L~~~i~k~V~V~L~~g----~~~~G~L~~~D~~mNlvL~   47 (88)
                      ||+.-.-|+   .-+..++|+.|.|+|++.    +.++|+|.++|+. ++.|.
T Consensus        81 SSPGldRpL~~~~df~r~~G~~v~V~l~~~~~~~~~~~G~L~~~~~~-~v~l~  132 (155)
T PRK14646         81 SSQGVSDELTSERDFKTFKGFPVNVELNQKNSKIKFLNGLLYEKSKD-YLAIN  132 (155)
T ss_pred             cCCCCCCcCCCHHHHHHhCCCEEEEEEecCcCCeEEEEEEEEEEeCC-EEEEE
Confidence            666666665   456778999999999653    7889999999985 45553

>PRK14647 hypothetical protein; Provisional

Probab=92.92  E-value=0.35  Score=32.87  Aligned_cols=40  Identities=18%  Similarity=0.076  Sum_probs=31.9

Q ss_pred             CCCCCCCcH---HHHhhcCCCEEEEEEc---------CccEEEEEEEEecCC
Q psy6372           2 STPLPCNPK---PFLNLLTGKSVICKLK---------WGHEYKGILVSTDGY   41 (88)
Q Consensus         2 ~~~~~~~p~---~~L~~~i~k~V~V~L~---------~g~~~~G~L~~~D~~   41 (88)
                      ||+...-|+   .-+..++|+.|.|+|+         +.+.+.|+|.++|+.
T Consensus        80 SSPG~~RpL~~~~~f~r~~G~~v~V~l~~~~~~~~~~~~~~~~G~L~~~~~~  131 (159)
T PRK14647         80 SSPGLDRPLKKEADYERYAGRLVKVRTFELLADEAGNKRKTFLGELEGLADG  131 (159)
T ss_pred             cCCCCCCcCCCHHHHHHhCCcEEEEEEeccccccccCCceEEEEEEEeecCC
Confidence            666666665   4567789999999995         359999999999963

>PRK14637 hypothetical protein; Provisional

Probab=92.14  E-value=0.48  Score=32.07  Aligned_cols=45  Identities=16%  Similarity=0.181  Sum_probs=33.1

Q ss_pred             CCCCCCCcH---HHHhhcCCCEEEEEEcCccEE-EEEEEEecCCcceEEc
Q psy6372           2 STPLPCNPK---PFLNLLTGKSVICKLKWGHEY-KGILVSTDGYMNCQLA   47 (88)
Q Consensus         2 ~~~~~~~p~---~~L~~~i~k~V~V~L~~g~~~-~G~L~~~D~~mNlvL~   47 (88)
                      ||+...-|+   .-+..++|+.|.|++.+.+.+ +|+|.++|+. ++.|.
T Consensus        79 SSPGldRpL~~~~~f~r~~G~~V~V~l~~~~~~~~G~L~~~~d~-~v~l~  127 (151)
T PRK14637         79 SSPGIERVIKNAAEFSIFVGETVKVWFECTGQWQVGTIAEADET-CLVLT  127 (151)
T ss_pred             eCCCCCCCCCCHHHHHHhCCCEEEEEECCCCcEEEEEEEEEeCC-EEEEE
Confidence            666666665   456777999999999544556 7999999985 45554

>PRK14631 hypothetical protein; Provisional

Probab=92.12  E-value=0.48  Score=32.84  Aligned_cols=38  Identities=24%  Similarity=0.245  Sum_probs=31.0

Q ss_pred             CCCCCCCcH---HHHhhcCCCEEEEEEc----CccEEEEEEEEec
Q psy6372           2 STPLPCNPK---PFLNLLTGKSVICKLK----WGHEYKGILVSTD   39 (88)
Q Consensus         2 ~~~~~~~p~---~~L~~~i~k~V~V~L~----~g~~~~G~L~~~D   39 (88)
                      ||+.-.-|+   .-+..++|+.|.|+|.    +.+.++|+|.++|
T Consensus        98 SSPGldRpL~~~~df~r~~G~~V~V~l~~~~~~~k~~~G~L~~v~  142 (174)
T PRK14631         98 SSPGWDRPFFQLEQLQGYIGQQVALRLIAAVENRRKFQAKLLAVD  142 (174)
T ss_pred             eCCCCCCcCCCHHHHHHhCCCeEEEEEecccCCceEEEEEEEEee
Confidence            666666665   4667789999999996    4599999999998

>PRK06955 biotin--protein ligase; Provisional

Probab=91.29  E-value=1.1  Score=33.19  Aligned_cols=50  Identities=18%  Similarity=0.183  Sum_probs=36.4

Q ss_pred             cCCCEEEEEEcCccEEEEEEEEecCCcceEEcceEEEecCeeeeeeceEEEeCC
Q psy6372          16 LTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTGKLGEVLIRCN   69 (88)
Q Consensus        16 ~i~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~d~~e~~~~~~~~~~~~v~IrG~   69 (88)
                      ++|++|+|...+++.+.|++.++|+...|+++...    |......|.|.+|..
T Consensus       247 ~~g~~V~v~~~~~~~~~G~~~gId~~G~L~v~~~~----g~~~~~sGeV~~~~~  296 (300)
T PRK06955        247 YAGREVVLLEDGAELARGVAHGIDETGQLLLDTPA----GRQAIAAGDVSLREA  296 (300)
T ss_pred             cCCCeEEEEECCCcEEEEEEeeECCCceEEEEeCC----CeEEEEEEEEEEecc
Confidence            57999999776778899999999999999985322    212344566666544

>PRK14641 hypothetical protein; Provisional

Probab=91.21  E-value=0.6  Score=32.37  Aligned_cols=38  Identities=21%  Similarity=0.175  Sum_probs=30.3

Q ss_pred             CCCCCCCcHH---HHhhcCCCEEEEEEcC----ccEEEEEEEEec
Q psy6372           2 STPLPCNPKP---FLNLLTGKSVICKLKW----GHEYKGILVSTD   39 (88)
Q Consensus         2 ~~~~~~~p~~---~L~~~i~k~V~V~L~~----g~~~~G~L~~~D   39 (88)
                      ||+...-|+.   -+.+++|+.|.|+|.+    .+.++|+|.+++
T Consensus        85 SSPGldRpL~~~~~f~r~~G~~V~V~l~~~~~~~~~~~G~L~~~~  129 (173)
T PRK14641         85 SSPGLGEPIILPRQYGRHVGRLLRVTYRDEEGSEHEVTGHLQEVS  129 (173)
T ss_pred             eCCCCCCcCCCHHHHHHhCCCEEEEEEecccCCeEEEEEEEEeee
Confidence            5666666654   5677799999999976    468999999996

>KOG1073|consensus

Probab=91.06  E-value=0.76  Score=35.39  Aligned_cols=65  Identities=18%  Similarity=0.168  Sum_probs=51.3

Q ss_pred             hhcCCCEEEEEEcCccEEEEEEEEec-CCcceEEcceEEE-ecC-----e----eeeeeceEEEeCCcEEEEEcCC
Q psy6372          14 NLLTGKSVICKLKWGHEYKGILVSTD-GYMNCQLASTEEI-IDG-----H----CTGKLGEVLIRCNNILYIRGAE   78 (88)
Q Consensus        14 ~~~i~k~V~V~L~~g~~~~G~L~~~D-~~mNlvL~d~~e~-~~~-----~----~~~~~~~v~IrG~~I~~I~~~d   78 (88)
                      ..+||+.|.+.-+++..|.|.|..+| +..-|-|.+|-.+ .++     .    ...-++.++.||+.|.-+.+-+
T Consensus         5 t~yIGS~ISLISk~DIRYEGILy~in~qdSTlgLqnVRsfGTEgRk~~~pq~p~~~kVy~YIlFRGSDIKDL~V~~   80 (361)
T KOG1073|consen    5 TSYIGSFISLISKNDIRYEGILYTINLQDSTLGLQNVRSFGTEGRKTDGPQVPPDDKVYDYILFRGSDIKDLIVQE   80 (361)
T ss_pred             cccccceeEEeecccceeeeEEEeccccccceehhheeecccccCCCCCCcCCCCccceeeEEecCcccceeeecc
Confidence            46899999999999999999999999 7788999998533 211     1    1226789999999999766543

>PRK11886 bifunctional biotin--[acetyl-CoA-carboxylase] synthetase/biotin operon repressor; Provisional

Probab=88.84  E-value=2.5  Score=31.16  Aligned_cols=48  Identities=21%  Similarity=0.174  Sum_probs=34.7

Q ss_pred             cCCCEEEEEEcCccEEEEEEEEecCCcceEEcceEEEecCeeeeeeceEEEeC
Q psy6372          16 LTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTGKLGEVLIRC   68 (88)
Q Consensus        16 ~i~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~d~~e~~~~~~~~~~~~v~IrG   68 (88)
                      +.|++|++... +..+.|++.++|+...|+++..    .+......|.+.+++
T Consensus       270 ~~g~~v~~~~~-~~~~~G~~~gi~~~G~L~i~~~----g~~~~~~~gev~~~~  317 (319)
T PRK11886        270 FLGREVKLIIG-DKEISGIARGIDEQGALLLEDD----GVEKPFNGGEISLRS  317 (319)
T ss_pred             ccCCeEEEEeC-CcEEEEEEEEECCCceEEEEeC----CcEEEEEEeEEEEec
Confidence            57999999874 5679999999999999999621    112334556666654

>PRK14630 hypothetical protein; Provisional

Probab=87.59  E-value=1.8  Score=29.05  Aligned_cols=43  Identities=16%  Similarity=0.132  Sum_probs=32.0

Q ss_pred             CCCCCCCcH---HHHhhcCCCEEEEEEcCccEEEEEEEEecCCcceEE
Q psy6372           2 STPLPCNPK---PFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQL   46 (88)
Q Consensus         2 ~~~~~~~p~---~~L~~~i~k~V~V~L~~g~~~~G~L~~~D~~mNlvL   46 (88)
                      ||+.-.-|+   .-+..++|++|.|+|.. ...+|+|.++|+.. +.|
T Consensus        78 SSPGldRpL~~~~df~r~~G~~v~V~l~~-~~~~G~L~~~~d~~-i~l  123 (143)
T PRK14630         78 STPGINRKIKSDREFKIFEGKKIKLMLDN-DFEEGFILEAKADS-FIF  123 (143)
T ss_pred             eCCCCCCcCCCHHHHHHhCCCEEEEEEcC-cceEEEEEEEeCCE-EEE
Confidence            666666665   45667799999999965 44599999999843 444

>TIGR00121 birA_ligase birA, biotin-[acetyl-CoA-carboxylase] ligase region

Probab=87.52  E-value=3.4  Score=29.26  Aligned_cols=31  Identities=23%  Similarity=0.099  Sum_probs=27.1

Q ss_pred             cCCCEEEEEEcCccEEEEEEEEecCCcceEEc
Q psy6372          16 LTGKSVICKLKWGHEYKGILVSTDGYMNCQLA   47 (88)
Q Consensus        16 ~i~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~   47 (88)
                      .+|++|++...+ ..+.|+..++|+...|+++
T Consensus       191 ~~g~~V~v~~~~-~~~~G~~~gI~~~G~L~v~  221 (237)
T TIGR00121       191 HIGREVSLTTGN-GEIEGIARGIDKDGALLLE  221 (237)
T ss_pred             ccCCeEEEEeCC-cEEEEEEEeECCCceEEEE
Confidence            469999998754 5799999999999999996

The protein name suggests that this enzyme transfers biotin only to acetyl-CoA-carboxylase but it also transfers the biotin moiety to other proteins. The apparent orthologs among the eukaryotes are larger proteins that contain a single copy of this domain.

>PRK14635 hypothetical protein; Provisional

Probab=87.37  E-value=3  Score=28.40  Aligned_cols=45  Identities=20%  Similarity=0.193  Sum_probs=33.1

Q ss_pred             CCCCCCCcH---HHHhhcCCCEEEEEEc--CccEEEE---EEEEecCCcceEEc
Q psy6372           2 STPLPCNPK---PFLNLLTGKSVICKLK--WGHEYKG---ILVSTDGYMNCQLA   47 (88)
Q Consensus         2 ~~~~~~~p~---~~L~~~i~k~V~V~L~--~g~~~~G---~L~~~D~~mNlvL~   47 (88)
                      ||+.-.-|+   .-+..++|+.|.|++.  ++..++|   +|.++|+. ++.|.
T Consensus        80 SSPGldRpL~~~~~~~r~~G~~v~v~~~~~~~~~~~g~~g~L~~~~~~-~v~l~  132 (162)
T PRK14635         80 SSAGAERKLRLPEDLDRFRGIPVRLVFRSEESEKWQEGIFRLVNRDGD-QVELE  132 (162)
T ss_pred             cCCCCCCcCCCHHHHHHhCCCEEEEEEecCCCcEEEecceEEEEEcCC-EEEEE
Confidence            666666665   4567789999999985  4678888   99999975 45443

>PRK13325 bifunctional biotin--[acetyl-CoA-carboxylase] ligase/pantothenate kinase; Reviewed

Probab=86.17  E-value=5.4  Score=32.39  Aligned_cols=32  Identities=22%  Similarity=0.219  Sum_probs=28.5

Q ss_pred             cCCCEEEEEEcCccEEEEEEEEecCCcceEEc
Q psy6372          16 LTGKSVICKLKWGHEYKGILVSTDGYMNCQLA   47 (88)
Q Consensus        16 ~i~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~   47 (88)
                      +.|++|.+...++..+.|+..++|+...|.|+
T Consensus       276 ~~gk~V~v~~~~~~~~~Gi~~GId~~G~L~l~  307 (592)
T PRK13325        276 DHGKAVLLLRDGETVFEGTVKGVDGQGVLHLE  307 (592)
T ss_pred             cCCCeEEEEeCCCcEEEEEEEEECCCCEEEEE
Confidence            57999999766777899999999999999996

>PF03614 Flag1_repress: Repressor of phase-1 flagellin; InterPro: IPR003223 Flagellin is the subunit which polymerises to form the filaments of bacterial flagella

Probab=83.28  E-value=2  Score=29.58  Aligned_cols=34  Identities=15%  Similarity=-0.042  Sum_probs=31.1

Q ss_pred             CCCEEEEEEcCccEEEEEEEEecCCcceEEcceE
Q psy6372          17 TGKSVICKLKWGHEYKGILVSTDGYMNCQLASTE   50 (88)
Q Consensus        17 i~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~d~~   50 (88)
                      -+-+|+|.+.||..+.|.+.+|+.--|.+|..+.
T Consensus        28 ~~~pVrvv~~ng~~f~myV~gf~~~~n~iL~p~~   61 (165)
T PF03614_consen   28 NDIPVRVVSENGQVFCMYVSGFMSKENKILAPDP   61 (165)
T ss_pred             cCCceEEEecCCcEEEEEEeccCcccCEEeccCC
Confidence            4678999999999999999999999999998766

The proteins in this family are transcriptional repressors of phase-1 flagellin genes.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent

>PRK09618 flgD flagellar basal body rod modification protein; Provisional

Probab=81.76  E-value=3  Score=28.14  Aligned_cols=26  Identities=27%  Similarity=0.230  Sum_probs=24.0

Q ss_pred             hhcCCCEEEEEEcCccEEEEEEEEec
Q psy6372          14 NLLTGKSVICKLKWGHEYKGILVSTD   39 (88)
Q Consensus        14 ~~~i~k~V~V~L~~g~~~~G~L~~~D   39 (88)
                      ..++||.|.+...+|..++|++.++-
T Consensus        88 ~slVGk~V~~~~~~g~~~tG~V~~V~  113 (142)
T PRK09618         88 SELIGKEVEWEGEDGEIVSGTVTSVK  113 (142)
T ss_pred             HHHhCCEEEEEeCCCCEEEEEEEEEE
Confidence            46899999999999999999999986

>COG0340 BirA Biotin-(acetyl-CoA carboxylase) ligase [Coenzyme metabolism]

Probab=81.30  E-value=10  Score=27.32  Aligned_cols=35  Identities=29%  Similarity=0.213  Sum_probs=31.8

Q ss_pred             hcCCCEEEEEEcCccEEEEEEEEecCCcceEEcce
Q psy6372          15 LLTGKSVICKLKWGHEYKGILVSTDGYMNCQLAST   49 (88)
Q Consensus        15 ~~i~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~d~   49 (88)
                      ..+|++|+++..++....|+..++|....|+++..
T Consensus       187 ~~~g~~V~~~~~~~~~~gg~a~~id~~G~L~l~~~  221 (238)
T COG0340         187 LSLGKEVRLTLGGGVIFGGIAKGIDEDGALLLETD  221 (238)
T ss_pred             ccCCCEEEEEeCCCcEeeeEEEEECCCceEEEEeC
Confidence            34899999999999999999999999999998766

>PF11607 DUF3247: Protein of unknown function (DUF3247); InterPro: IPR021649 This family of proteins is the protein product of the gene XC5848 from Xanthomonas campestris

Probab=80.18  E-value=2.9  Score=26.58  Aligned_cols=19  Identities=21%  Similarity=0.263  Sum_probs=15.2

Q ss_pred             CCEEEEEEcCccEEEEEEE
Q psy6372          18 GKSVICKLKWGHEYKGILV   36 (88)
Q Consensus        18 ~k~V~V~L~~g~~~~G~L~   36 (88)
                      +.+|.++|+||+.+.||+.
T Consensus        28 e~~V~l~L~DGs~l~Gtv~   46 (101)
T PF11607_consen   28 EERVELELDDGSMLRGTVA   46 (101)
T ss_dssp             T-EEEEEETTS-EEEEEEC
T ss_pred             cceEEEEEcCCCeeeeeec
Confidence            4689999999999999974

The protein has no known function however its structure has been determined. The protein adopts a Lsm fold however differences with the fold were observed at the N-terminal and internal regions []. ; PDB: 2E12_B.

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	88
3cw1_F	86	Crystal Structure Of Human Spliceosomal U1 Snrnp Le		7e-27
1n9r_A	93	Crystal Structure Of A Heptameric Ring Complex Of Y		7e-17
1n9s_A	93	Crystal Structure Of Yeast Smf In Spacegroup P43212		3e-16
3swn_B	77	Structure Of The Lsm657 Complex: An Assembly Interm		7e-13
4emk_B	75	Crystal Structure Of Splsm567 Length = 75		7e-12
1loj_A	87	Crystal Structure Of A Methanobacterial Sm-Like Arc		1e-09
1jbm_A	86	Heptameric Crystal Structure Of Mth649, An Sm-Like		1e-09
1jri_A	85	The Crystal Structure Of An Sm-Like Archaeal Protei		1e-09
1i81_A	83	Crystal Structure Of A Heptameric Lsm Protein From		2e-09
1i5l_A	77	Crystal Structure Of An Sm-Like Protein (Af-Sm1) Fr		8e-08
1i8f_A	81	The Crystal Structure Of A Heptameric Archaeal Sm P		9e-08
1h64_1	75	Crystal Structure Of The Sm-Related Protein Of P. A		2e-06
1m8v_A	77	Structure Of Pyrococcus Abyssii Sm Protein In Compl		2e-06
1th7_A	81	Crystal Structure Of An Archaeal Sm Protein From Su		2e-05
4emh_A	105	Crystal Structure Of Splsm4 Length = 105		6e-04

>pdb|3CW1|F Chain F, Crystal Structure Of Human Spliceosomal U1 Snrnp Length = 86

Iteration: 1
 Score =  115 bits (288), Expect = 7e-27,   Method: Compositional matrix adjust.
 Identities = 55/71 (77%), Positives = 59/71 (83%)
Query: 5  LPCNPKPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTGKLGEV 64
          LP NPKPFLN LTGK V+ KLKWG EYKG LVS DGYMN QLA+TEE IDG  +G LGEV
Sbjct: 3  LPLNPKPFLNGLTGKPVMVKLKWGMEYKGYLVSVDGYMNMQLANTEEYIDGALSGHLGEV 62
Query: 65 LIRCNNILYIR 75
          LIRCNN+LYIR
Sbjct: 63 LIRCNNVLYIR 73

>pdb|1N9R|A Chain A, Crystal Structure Of A Heptameric Ring Complex Of Yeast Smf In Spacegroup P4122 Length = 93

Iteration: 1
 Score = 82.0 bits (201), Expect = 7e-17,   Method: Compositional matrix adjust.
 Identities = 41/76 (53%), Positives = 47/76 (61%), Gaps = 1/76 (1%)
Query: 1  MSTPLPCNPKPFLNLLTGKSVICKLKWGH-EYKGILVSTDGYMNCQLASTEEIIDGHCTG 59
          +S   P NPKPFL  L    V  KLK+   EY+G LVSTD Y N QL   EE + G   G
Sbjct: 14 ISAMQPVNPKPFLKGLVNHRVGVKLKFNSTEYRGTLVSTDNYFNLQLNEAEEFVAGVSHG 73
Query: 60 KLGEVLIRCNNILYIR 75
           LGE+ IRCNN+LYIR
Sbjct: 74 TLGEIFIRCNNVLYIR 89

>pdb|1N9S|A Chain A, Crystal Structure Of Yeast Smf In Spacegroup P43212 Length = 93

Iteration: 1
 Score = 80.1 bits (196), Expect = 3e-16,   Method: Compositional matrix adjust.
 Identities = 40/76 (52%), Positives = 46/76 (60%), Gaps = 1/76 (1%)
Query: 1  MSTPLPCNPKPFLNLLTGKSVICKLKWGH-EYKGILVSTDGYMNCQLASTEEIIDGHCTG 59
          +S   P NPKPFL  L    V  KLK+   EY+G LVSTD Y N QL   EE + G   G
Sbjct: 14 ISAMQPVNPKPFLKGLVNHRVGVKLKFNSTEYRGTLVSTDNYFNLQLNEAEEFVAGVSHG 73
Query: 60 KLGEVLIRCNNILYIR 75
           LGE+ IR NN+LYIR
Sbjct: 74 TLGEIFIRSNNVLYIR 89

>pdb|3SWN|B Chain B, Structure Of The Lsm657 Complex: An Assembly Intermediate Of The Lsm1 7 And Lsm2 8 Rings Length = 77

Iteration: 1
 Score = 68.9 bits (167), Expect = 7e-13,   Method: Compositional matrix adjust.
 Identities = 32/70 (45%), Positives = 43/70 (61%)
Query: 5  LPCNPKPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTGKLGEV 64
          +  +P  FLN + GK V+ +L  G +YKGIL   DGYMN  L  TEE ++G  T   G+ 
Sbjct: 3  MDSSPNEFLNKVIGKKVLIRLSSGVDYKGILSCLDGYMNLALERTEEYVNGKKTNVYGDA 62
Query: 65 LIRCNNILYI 74
           IR NN+LY+
Sbjct: 63 FIRGNNVLYV 72

>pdb|4EMK|B Chain B, Crystal Structure Of Splsm567 Length = 75

Iteration: 1
 Score = 65.5 bits (158), Expect = 7e-12,   Method: Compositional matrix adjust.
 Identities = 31/69 (44%), Positives = 41/69 (59%)
Query: 6  PCNPKPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTGKLGEVL 65
            +P  FLN + GK V+ +L  G +YKGIL   DGY N  L  TEE ++G  T   G+  
Sbjct: 2  DSSPNEFLNKVIGKKVLIRLSSGVDYKGILSCLDGYXNLALERTEEYVNGKKTNVYGDAF 61
Query: 66 IRCNNILYI 74
          IR NN+LY+
Sbjct: 62 IRGNNVLYV 70

>pdb|1LOJ|A Chain A, Crystal Structure Of A Methanobacterial Sm-Like Archaeal Protein (Smap1) Bound To Uridine-5'-Monophosphate (Ump) Length = 87

Iteration: 1
 Score = 58.2 bits (139), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 28/54 (51%), Positives = 36/54 (66%)
Query: 21 VICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTGKLGEVLIRCNNILYI 74
          VI KLK   E++G+L S D +MN  L   EE+ DG  T +LG VLIR +NI+YI
Sbjct: 26 VIIKLKGDREFRGVLKSFDLHMNLVLNDAEELEDGEVTRRLGTVLIRGDNIVYI 79

>pdb|1JBM|A Chain A, Heptameric Crystal Structure Of Mth649, An Sm-Like Archaeal Protein From Methanobacterium Thermautotrophicum Length = 86

Iteration: 1
 Score = 58.2 bits (139), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 28/54 (51%), Positives = 36/54 (66%)
Query: 21 VICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTGKLGEVLIRCNNILYI 74
          VI KLK   E++G+L S D +MN  L   EE+ DG  T +LG VLIR +NI+YI
Sbjct: 26 VIIKLKGDREFRGVLKSFDLHMNLVLNDAEELEDGEVTRRLGTVLIRGDNIVYI 79

>pdb|1JRI|A Chain A, The Crystal Structure Of An Sm-Like Archaeal Protein With Two Heptamers In The Asymmetric Unit. Length = 85

Iteration: 1
 Score = 57.8 bits (138), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 28/54 (51%), Positives = 36/54 (66%)
Query: 21 VICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTGKLGEVLIRCNNILYI 74
          VI KLK   E++G+L S D +MN  L   EE+ DG  T +LG VLIR +NI+YI
Sbjct: 26 VIIKLKGDREFRGVLKSFDLHMNLVLNDAEELEDGEVTRRLGTVLIRGDNIVYI 79

>pdb|1I81|A Chain A, Crystal Structure Of A Heptameric Lsm Protein From Methanobacterium Thermoautotrophicum Length = 83

Iteration: 1
 Score = 57.8 bits (138), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 28/54 (51%), Positives = 36/54 (66%)
Query: 21 VICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTGKLGEVLIRCNNILYI 74
          VI KLK   E++G+L S D +MN  L   EE+ DG  T +LG VLIR +NI+YI
Sbjct: 28 VIIKLKGDREFRGVLKSFDLHMNLVLNDAEELEDGEVTRRLGTVLIRGDNIVYI 81

>pdb|1I5L|A Chain A, Crystal Structure Of An Sm-Like Protein (Af-Sm1) From Archaeoglobus Fulgidus Complexed With Short Poly-U Rna Length = 77

Iteration: 1
 Score = 52.0 bits (123), Expect = 8e-08,   Method: Compositional matrix adjust.
 Identities = 25/70 (35%), Positives = 38/70 (54%)
Query: 5  LPCNPKPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTGKLGEV 64
          +P  P   LN      VI +LK G E++G L   D +MN  L   EEI +G    K+G V
Sbjct: 1  MPPRPLDVLNRSLKSPVIVRLKGGREFRGTLDGYDIHMNLVLLDAEEIQNGEVVRKVGSV 60
Query: 65 LIRCNNILYI 74
          +IR + ++++
Sbjct: 61 VIRGDTVVFV 70

>pdb|1I8F|A Chain A, The Crystal Structure Of A Heptameric Archaeal Sm Protein: Implications For The Eukaryotic Snrnp Core Length = 81

Iteration: 1
 Score = 52.0 bits (123), Expect = 9e-08,   Method: Compositional matrix adjust.
 Identities = 26/57 (45%), Positives = 37/57 (64%), Gaps = 1/57 (1%)
Query: 18 GKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTGKLGEVLIRCNNILYI 74
          GK V+ KL+  HE +GIL S D ++N  L   EEIIDG+   K G +++R  N+L+I
Sbjct: 21 GKQVLVKLRDSHEIRGILRSFDQHVNLLLEDAEEIIDGNVY-KRGTMVVRGENVLFI 76

>pdb|1H64|1 Chain 1, Crystal Structure Of The Sm-Related Protein Of P. Abyssi The Biological Unit Is A Heptamer Length = 75

Iteration: 1
 Score = 47.4 bits (111), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 22/56 (39%), Positives = 34/56 (60%)
Query: 19 KSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTGKLGEVLIRCNNILYI 74
          K V+  LK G E++G L+  D ++N  LA  E I DG    + G+++IR +N+L I
Sbjct: 15 KDVLVILKKGFEFRGRLIGYDIHLNVVLADAEMIQDGEVVKRYGKIVIRGDNVLAI 70

>pdb|1M8V|A Chain A, Structure Of Pyrococcus Abyssii Sm Protein In Complex With A Uridine Heptamer Length = 77

Iteration: 1
 Score = 47.0 bits (110), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 22/56 (39%), Positives = 34/56 (60%)
Query: 19 KSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTGKLGEVLIRCNNILYI 74
          K V+  LK G E++G L+  D ++N  LA  E I DG    + G+++IR +N+L I
Sbjct: 17 KDVLVILKKGFEFRGRLIGYDIHLNVVLADAEMIQDGEVVKRYGKIVIRGDNVLAI 72

>pdb|1TH7|A Chain A, Crystal Structure Of An Archaeal Sm Protein From Sulfolobus Solfataricus Length = 81

Iteration: 1
 Score = 44.3 bits (103), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 22/54 (40%), Positives = 33/54 (61%)
Query: 21 VICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTGKLGEVLIRCNNILYI 74
          V+ KLK   E +G+L S D +MN  L+ +EEI       KLG ++IR +N++ I
Sbjct: 22 VLVKLKGNKEVRGMLRSYDQHMNLVLSDSEEIQSDGSGKKLGTIVIRGDNVILI 75

>pdb|4EMH|A Chain A, Crystal Structure Of Splsm4 Length = 105

Iteration: 1
 Score = 39.3 bits (90), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 27/74 (36%), Positives = 36/74 (48%), Gaps = 7/74 (9%)
Query: 6  PCNPKPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEII----DGHCTGKL 61
          P  P   LN   G+ ++ +LK G  + G L + D Y N  L    E+I    DG    +L
Sbjct: 14 PXLPLTLLNATQGRPILVELKNGETFNGHLENCDNYXNLTL---REVIRTXPDGDKFFRL 70
Query: 62 GEVLIRCNNILYIR 75
           E  IR NNI Y+R
Sbjct: 71 PECYIRGNNIKYLR 84

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	88
3s6n_F	86	Small nuclear ribonucleoprotein F; SMN complex, SM	2e-36
1n9r_A	93	SMF, small nuclear ribonucleoprotein F, snRNP-F, S	2e-34
4emk_B	75	U6 snRNA-associated SM-like protein LSM6; SM fold,	5e-33
1h64_1	75	SnRNP SM-like protein; SM fold, spliceosome, snRNP	5e-30
1i4k_A	77	Putative snRNP SM-like protein; core snRNP domain,	7e-30
4emh_A	105	Probable U6 snRNA-associated SM-like protein LSM4;	6e-29
1mgq_A	83	SM-like protein; LSM, RNA-binding, archea, RNA bin	1e-28
1th7_A	81	SnRNP-2, small nuclear riboprotein protein; archae	3e-27
1ljo_A	77	Archaeal SM-like protein AF-SM2; snRNP, core snRNP	4e-27
1i8f_A	81	Putative snRNP SM-like protein; beta barrel-like S	7e-27
1d3b_A	75	Protein (small nuclear ribonucleoprotein SM D3); s	5e-21
1b34_A	119	Protein (small nuclear ribonucleoprotein SM D1); s	8e-21
2y9a_D	126	Small nuclear ribonucleoprotein SM D3; splicing-RN	1e-20
3s6n_G	76	Small nuclear ribonucleoprotein G; SMN complex, SM	4e-18
4emk_C	113	U6 snRNA-associated SM-like protein LSM7; SM fold,	2e-11
4emk_A	94	U6 snRNA-associated SM-like protein LSM5; SM fold,	3e-11
4emg_A	93	Probable U6 snRNA-associated SM-like protein LSM3;	1e-10
3bw1_A	96	SMX4 protein, U6 snRNA-associated SM-like protein	4e-09
3s6n_E	92	Small nuclear ribonucleoprotein E; SMN complex, SM	6e-09
2fwk_A	121	U6 snRNA-associated SM-like protein LSM5; structur	3e-07
1d3b_B	91	Protein (small nuclear ribonucleoprotein associat	2e-05

>3s6n_F Small nuclear ribonucleoprotein F; SMN complex, SMN-gemin2 complex, U-rich snRNA, SM fold, SM C SNRNPS, snRNP biogenesis, PRE-mRNA splicing; 2.50A {Homo sapiens} PDB: 2y9b_F 2y9c_F 2y9d_F 3cw1_F 3pgw_F* 2y9a_F Length = 86

 Score =  117 bits (294), Expect = 2e-36
 Identities = 66/88 (75%), Positives = 72/88 (81%), Gaps = 2/88 (2%)

Query: 1  MSTPLPCNPKPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTGK 60
          MS PL  NPKPFLN LTGK V+ KLKWG EYKG LVS DGYMN QLA+TEE IDG  +G 
Sbjct: 1  MSLPL--NPKPFLNGLTGKPVMVKLKWGMEYKGYLVSVDGYMNMQLANTEEYIDGALSGH 58

Query: 61 LGEVLIRCNNILYIRGAEEGDEEGEMRE 88
          LGEVLIRCNN+LYIRG EE +E+GEMRE
Sbjct: 59 LGEVLIRCNNVLYIRGVEEEEEDGEMRE 86

>1n9r_A SMF, small nuclear ribonucleoprotein F, snRNP-F, SM protein F; heptamer, translation; 2.80A {Saccharomyces cerevisiae} SCOP: b.38.1.1 PDB: 1n9s_A Length = 93

 Score =  112 bits (281), Expect = 2e-34
 Identities = 41/80 (51%), Positives = 47/80 (58%), Gaps = 1/80 (1%)

Query: 1  MSTPLPCNPKPFLNLLTGKSVICKLKW-GHEYKGILVSTDGYMNCQLASTEEIIDGHCTG 59
          +S   P NPKPFL  L    V  KLK+   EY+G LVSTD Y N QL   EE + G   G
Sbjct: 14 ISAMQPVNPKPFLKGLVNHRVGVKLKFNSTEYRGTLVSTDNYFNLQLNEAEEFVAGVSHG 73

Query: 60 KLGEVLIRCNNILYIRGAEE 79
           LGE+ IRCNN+LYIR    
Sbjct: 74 TLGEIFIRCNNVLYIRELPN 93

>4emk_B U6 snRNA-associated SM-like protein LSM6; SM fold, mRNA decay and PRE-mRNA splicing, LSM proteins, RNA protein; 2.30A {Schizosaccharomyces pombe} PDB: 3swn_B Length = 75

 Score =  107 bits (270), Expect = 5e-33
 Identities = 32/74 (43%), Positives = 44/74 (59%)

Query: 6  PCNPKPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTGKLGEVL 65
            +P  FLN + GK V+ +L  G +YKGIL   DGYMN  L  TEE ++G  T   G+  
Sbjct: 2  DSSPNEFLNKVIGKKVLIRLSSGVDYKGILSCLDGYMNLALERTEEYVNGKKTNVYGDAF 61

Query: 66 IRCNNILYIRGAEE 79
          IR NN+LY+   ++
Sbjct: 62 IRGNNVLYVSALDD 75

>1h64_1 SnRNP SM-like protein; SM fold, spliceosome, snRNP core; 1.9A {Pyrococcus abyssi} SCOP: b.38.1.1 PDB: 1m8v_A* Length = 75

 Score =  100 bits (251), Expect = 5e-30
 Identities = 25/72 (34%), Positives = 39/72 (54%)

Query: 8  NPKPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTGKLGEVLIR 67
           P   ++    K V+  LK G E++G L+  D ++N  LA  E I DG    + G+++IR
Sbjct: 4  RPLDVIHRSLDKDVLVILKKGFEFRGRLIGYDIHLNVVLADAEMIQDGEVVKRYGKIVIR 63

Query: 68 CNNILYIRGAEE 79
           +N+L I   EE
Sbjct: 64 GDNVLAISPTEE 75

>1i4k_A Putative snRNP SM-like protein; core snRNP domain, RNA binding protein; HET: CIT; 2.50A {Archaeoglobus fulgidus} SCOP: b.38.1.1 PDB: 1i5l_A* Length = 77

 Score =  100 bits (250), Expect = 7e-30
 Identities = 27/75 (36%), Positives = 39/75 (52%)

Query: 6  PCNPKPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTGKLGEVL 65
          P  P   LN      VI +LK G E++G L   D +MN  L   EEI +G    K+G V+
Sbjct: 2  PPRPLDVLNRSLKSPVIVRLKGGREFRGTLDGYDIHMNLVLLDAEEIQNGEVVRKVGSVV 61

Query: 66 IRCNNILYIRGAEEG 80
          IR + ++++  A  G
Sbjct: 62 IRGDTVVFVSPAPGG 76

>4emh_A Probable U6 snRNA-associated SM-like protein LSM4; SM fold, mRNA decay, PRE-mRNA splicing, LSM proteins, RNA BI protein; 2.20A {Schizosaccharomyces pombe} Length = 105

 Score = 98.7 bits (246), Expect = 6e-29
 Identities = 27/79 (34%), Positives = 38/79 (48%), Gaps = 1/79 (1%)

Query: 2  STPLPCNPKPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLAS-TEEIIDGHCTGK 60
           +  P  P   LN   G+ ++ +LK G  + G L + D YMN  L      + DG    +
Sbjct: 10 HSQDPMLPLTLLNATQGRPILVELKNGETFNGHLENCDNYMNLTLREVIRTMPDGDKFFR 69

Query: 61 LGEVLIRCNNILYIRGAEE 79
          L E  IR NNI Y+R  +E
Sbjct: 70 LPECYIRGNNIKYLRIQDE 88

>1mgq_A SM-like protein; LSM, RNA-binding, archea, RNA binding protein; 1.70A {Methanothermobacterthermautotrophicus} SCOP: b.38.1.1 PDB: 1i81_A 1loj_A* 1jbm_A 1jri_A Length = 83

 Score = 97.0 bits (242), Expect = 1e-28
 Identities = 30/73 (41%), Positives = 38/73 (52%)

Query: 2  STPLPCNPKPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTGKL 61
                 P   L       VI KLK   E++G+L S D +MN  L   EE+ DG  T +L
Sbjct: 9  QRVNVQRPLDALGNSLNSPVIIKLKGDREFRGVLKSFDLHMNLVLNDAEELEDGEVTRRL 68

Query: 62 GEVLIRCNNILYI 74
          G VLIR +NI+YI
Sbjct: 69 GTVLIRGDNIVYI 81

>1th7_A SnRNP-2, small nuclear riboprotein protein; archaea, SM protein, SM fold, SS-SM1, RNA binding protein; 1.68A {Sulfolobus solfataricus} SCOP: b.38.1.1 Length = 81

 Score = 93.9 bits (234), Expect = 3e-27
 Identities = 24/78 (30%), Positives = 37/78 (47%), Gaps = 1/78 (1%)

Query: 1  MSTPLPCNPKPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTGK 60
          M+          L       V+ KLK   E +G+L S D +MN  L+ +EEI       K
Sbjct: 3  MNFL-AETAHKVLAESLNNLVLVKLKGNKEVRGMLRSYDQHMNLVLSDSEEIQSDGSGKK 61

Query: 61 LGEVLIRCNNILYIRGAE 78
          LG ++IR +N++ I   +
Sbjct: 62 LGTIVIRGDNVILISPLQ 79

>1ljo_A Archaeal SM-like protein AF-SM2; snRNP, core snRNP domain, RNA binding protein, unknown F; 1.95A {Archaeoglobus fulgidus} SCOP: b.38.1.1 Length = 77

 Score = 93.1 bits (232), Expect = 4e-27
 Identities = 21/73 (28%), Positives = 35/73 (47%), Gaps = 1/73 (1%)

Query: 8  NPKPFLNLLTGKSVICKLKWG-HEYKGILVSTDGYMNCQLASTEEIIDGHCTGKLGEVLI 66
           P   +  + GK +  ++K   ++  G L   D YMN  L +  E         LGE+++
Sbjct: 5  LPNQMVKSMVGKIIRVEMKGEENQLVGKLEGVDDYMNLYLTNAMECKGEEKVRSLGEIVL 64

Query: 67 RCNNILYIRGAEE 79
          R NN++ I+  EE
Sbjct: 65 RGNNVVLIQPQEE 77

>1i8f_A Putative snRNP SM-like protein; beta barrel-like SMAP monomers form 35-stranded beta-sheet I heptamer, structural genomics; 1.75A {Pyrobaculum aerophilum} SCOP: b.38.1.1 PDB: 1lnx_A* Length = 81

 Score = 92.8 bits (231), Expect = 7e-27
 Identities = 28/81 (34%), Positives = 41/81 (50%), Gaps = 4/81 (4%)

Query: 1  MST---PLPCNPKPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHC 57
          M++            L    GK V+ KL+  HE +GIL S D ++N  L   EEIIDG+ 
Sbjct: 1  MASDISKCFATLGATLQDSIGKQVLVKLRDSHEIRGILRSFDQHVNLLLEDAEEIIDGNV 60

Query: 58 TGKLGEVLIRCNNILYIRGAE 78
            K G +++R  N+L+I    
Sbjct: 61 Y-KRGTMVVRGENVLFISPVP 80

>1d3b_A Protein (small nuclear ribonucleoprotein SM D3); snRNP, splicing, core snRNP domain, systemic lupus eryth SLE, RNA binding protein; HET: CIT; 2.00A {Homo sapiens} SCOP: b.38.1.1 Length = 75

 Score = 77.8 bits (192), Expect = 5e-21
 Identities = 20/75 (26%), Positives = 33/75 (44%), Gaps = 3/75 (4%)

Query: 1  MSTPLPCNPKPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTGK 60
          MS  +P      L+   G  V C+   G  Y+G L+  +  MNCQ+++           +
Sbjct: 1  MSIGVP---IKVLHEAEGHIVTCETNTGEVYRGKLIEAEDNMNCQMSNITVTYRDGRVAQ 57

Query: 61 LGEVLIRCNNILYIR 75
          L +V IR   I ++ 
Sbjct: 58 LEQVYIRGCKIRFLI 72

>1b34_A Protein (small nuclear ribonucleoprotein SM D1); snRNP, splicing, spliceosome, core snRNP domain, systemi erythematosus, SLE, RNA binding protein; 2.50A {Homo sapiens} SCOP: b.38.1.1 PDB: 2y9a_B 2y9b_B 2y9c_B 2y9d_B 3cw1_B 3pgw_X* 3s6n_A Length = 119

 Score = 78.5 bits (193), Expect = 8e-21
 Identities = 19/64 (29%), Positives = 30/64 (46%)

Query: 12 FLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTGKLGEVLIRCNNI 71
          FL  L+ ++V  +LK G +  G +   D  MN  L + +  +      +L  + IR NNI
Sbjct: 6  FLMKLSHETVTIELKNGTQVHGTITGVDVSMNTHLKAVKMTLKNREPVQLETLSIRGNNI 65

Query: 72 LYIR 75
           Y  
Sbjct: 66 RYFI 69

>2y9a_D Small nuclear ribonucleoprotein SM D3; splicing-RNA complex, PRE-mRNA splicing, spliceosome, snRNP biogenesis, SM site, SM fold, heteromeric heptameric ring; 3.60A {Homo sapiens} PDB: 2y9b_D 2y9c_D 2y9d_D 3pgw_Z* 3cw1_D Length = 126

 Score = 78.2 bits (192), Expect = 1e-20
 Identities = 20/79 (25%), Positives = 35/79 (44%), Gaps = 3/79 (3%)

Query: 1  MSTPLPCNPKPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTGK 60
          MS  +P      L+   G  V C+   G  Y+G L+  +  MNCQ+++           +
Sbjct: 1  MSIGVP---IKVLHEAEGHIVTCETNTGEVYRGKLIEAEDNMNCQMSNITVTYRDGRVAQ 57

Query: 61 LGEVLIRCNNILYIRGAEE 79
          L +V IR + I ++   + 
Sbjct: 58 LEQVYIRGSKIRFLILPDM 76

>3s6n_G Small nuclear ribonucleoprotein G; SMN complex, SMN-gemin2 complex, U-rich snRNA, SM fold, SM C SNRNPS, snRNP biogenesis, PRE-mRNA splicing; 2.50A {Homo sapiens} PDB: 2y9b_G 2y9c_G 2y9d_G 3cw1_G 3pgw_G* 2y9a_G Length = 76

 Score = 70.4 bits (173), Expect = 4e-18
 Identities = 23/78 (29%), Positives = 33/78 (42%), Gaps = 4/78 (5%)

Query: 1  MSTPLPCNPKPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTGK 60
          MS   P    P L     K +  KL  G   +GIL   D +MN  +    E+        
Sbjct: 1  MSKAHP----PELKKFMDKKLSLKLNGGRHVQGILRGFDPFMNLVIDECVEMATSGQQNN 56

Query: 61 LGEVLIRCNNILYIRGAE 78
          +G V+IR N+I+ +   E
Sbjct: 57 IGMVVIRGNSIIMLEALE 74

>4emk_C U6 snRNA-associated SM-like protein LSM7; SM fold, mRNA decay and PRE-mRNA splicing, LSM proteins, RNA protein; 2.30A {Schizosaccharomyces pombe} PDB: 3swn_C Length = 113

 Score = 54.2 bits (130), Expect = 2e-11
 Identities = 20/78 (25%), Positives = 30/78 (38%), Gaps = 8/78 (10%)

Query: 13  LNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGH-------CTGKLGEVL 65
           L+    + +      G +  GIL   D  MN  L   EE +             KLG V+
Sbjct: 28  LSRYQDQRIQATFTGGRQITGILKGFDQLMNLVLDDVEEQLRNPEDGKLTGAIRKLGLVV 87

Query: 66  IRCNNILYIRGAEEGDEE 83
           +R   ++ I    +G EE
Sbjct: 88  VRGTTLVLI-APMDGSEE 104

>4emk_A U6 snRNA-associated SM-like protein LSM5; SM fold, mRNA decay and PRE-mRNA splicing, LSM proteins, RNA protein; 2.30A {Schizosaccharomyces pombe} PDB: 3swn_A Length = 94

 Score = 53.3 bits (128), Expect = 3e-11
 Identities = 19/75 (25%), Positives = 31/75 (41%), Gaps = 3/75 (4%)

Query: 1  MSTPLPCNPKPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEI-IDGHCTG 59
          MS  +   P   ++   G ++   +K   E+ G LV  D Y+N  L    E       T 
Sbjct: 15 MSMTIL--PLELIDKCIGSNLWVIMKSEREFAGTLVGFDDYVNIVLKDVTEYDTVTGVTE 72

Query: 60 KLGEVLIRCNNILYI 74
          K  E+L+  N +  +
Sbjct: 73 KHSEMLLNGNGMCML 87

>4emg_A Probable U6 snRNA-associated SM-like protein LSM3; SM fold, mRNA decay, LSM proteins, RNA binding protein; 2.70A {Schizosaccharomyces pombe} Length = 93

 Score = 52.1 bits (125), Expect = 1e-10
 Identities = 17/86 (19%), Positives = 30/86 (34%), Gaps = 13/86 (15%)

Query: 2  STPLPCNPKPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTG-- 59
          S      P   + L   + V  KL+   E  G L + D ++N  L   EEI+        
Sbjct: 3  SAQAVAEPLDLVRLSLDEIVYVKLRGDRELNGRLHAYDEHLNMVLGDAEEIVTIFDDEET 62

Query: 60 -----------KLGEVLIRCNNILYI 74
                         + +R ++++ I
Sbjct: 63 DKDKALKTIRKHYEMLFVRGDSVILI 88

>3bw1_A SMX4 protein, U6 snRNA-associated SM-like protein LSM3; RNA-binding protein, SM protein, ring, HOMO octamer, mRNA processing; 2.50A {Saccharomyces cerevisiae} Length = 96

 Score = 47.8 bits (114), Expect = 4e-09
 Identities = 18/88 (20%), Positives = 28/88 (31%), Gaps = 10/88 (11%)

Query: 8  NPKPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEII-------DGHCTGK 60
           P   L L   + V  KL+      G L + D + N  L+   E I             +
Sbjct: 10 TPLDLLKLNLDERVYIKLRGARTLVGTLQAFDSHCNIVLSDAVETIYQLNNEELSESERR 69

Query: 61 LGEVLIRCNNILYIRGAEEGDEEGEMRE 88
             V IR + +  I       E+ +   
Sbjct: 70 CEMVFIRGDTVTLI---STPSEDDDGAV 94

>3s6n_E Small nuclear ribonucleoprotein E; SMN complex, SMN-gemin2 complex, U-rich snRNA, SM fold, SM C SNRNPS, snRNP biogenesis, PRE-mRNA splicing; 2.50A {Homo sapiens} PDB: 2y9b_E 2y9c_E 2y9d_E 3cw1_E 3pgw_E* 2y9a_E Length = 92

 Score = 47.5 bits (113), Expect = 6e-09
 Identities = 15/64 (23%), Positives = 28/64 (43%), Gaps = 1/64 (1%)

Query: 12 FLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEI-IDGHCTGKLGEVLIRCNN 70
          +L   +   V    +     +G ++  D YMN  L   EEI        +LG ++++ +N
Sbjct: 24 YLQNRSRIQVWLYEQVNMRIEGCIIGFDEYMNLVLDDAEEIHSKTKSRKQLGRIMLKGDN 83

Query: 71 ILYI 74
          I  +
Sbjct: 84 ITLL 87

>2fwk_A U6 snRNA-associated SM-like protein LSM5; structural genomics, structural genomics consortium, SGC, DNA binding protein; 2.14A {Cryptosporidium parvum} SCOP: b.38.1.1 PDB: 3pgg_A Length = 121

 Score = 43.8 bits (103), Expect = 3e-07
 Identities = 15/81 (18%), Positives = 28/81 (34%), Gaps = 15/81 (18%)

Query: 9   PKPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTG--------- 59
           P   ++   G  +   +K   E+ G+L   D Y+N  L   +E                 
Sbjct: 29  PLALIDKCIGNRIYVVMKGDKEFSGVLRGFDEYVNMVLDDVQEYGFKADEEDISGGNKKL 88

Query: 60  ------KLGEVLIRCNNILYI 74
                 +L  +L+  NN+  +
Sbjct: 89  KRVMVNRLETILLSGNNVAML 109

>1d3b_B Protein (small nuclear ribonucleoprotein associat B); snRNP, splicing, core snRNP domain, systemic lupus eryth SLE, RNA binding protein; HET: CIT; 2.00A {Homo sapiens} SCOP: b.38.1.1 PDB: 2y9a_A 2y9b_A 2y9c_A 2y9d_A Length = 91

 Score = 38.7 bits (90), Expect = 2e-05
 Identities = 15/72 (20%), Positives = 27/72 (37%), Gaps = 10/72 (13%)

Query: 13 LNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEII----------DGHCTGKLG 62
          +       + C L+ G  + G   + D +MN  L   +E            +      LG
Sbjct: 9  MLQHIDYRMRCILQDGRIFIGTFKAFDKHMNLILCDCDEFRKIKPKNSKQAEREEKRVLG 68

Query: 63 EVLIRCNNILYI 74
           VL+R  N++ +
Sbjct: 69 LVLLRGENLVSM 80

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	88
3s6n_F	86	Small nuclear ribonucleoprotein F; SMN complex, SM	100.0
1i4k_A	77	Putative snRNP SM-like protein; core snRNP domain,	99.95
1d3b_A	75	Protein (small nuclear ribonucleoprotein SM D3); s	99.94
1h64_1	75	SnRNP SM-like protein; SM fold, spliceosome, snRNP	99.94
1th7_A	81	SnRNP-2, small nuclear riboprotein protein; archae	99.94
4emk_B	75	U6 snRNA-associated SM-like protein LSM6; SM fold,	99.94
1ljo_A	77	Archaeal SM-like protein AF-SM2; snRNP, core snRNP	99.94
1i8f_A	81	Putative snRNP SM-like protein; beta barrel-like S	99.94
4emh_A	105	Probable U6 snRNA-associated SM-like protein LSM4;	99.93
1n9r_A	93	SMF, small nuclear ribonucleoprotein F, snRNP-F, S	99.93
1mgq_A	83	SM-like protein; LSM, RNA-binding, archea, RNA bin	99.93
3s6n_G	76	Small nuclear ribonucleoprotein G; SMN complex, SM	99.92
3bw1_A	96	SMX4 protein, U6 snRNA-associated SM-like protein	99.92
4emk_A	94	U6 snRNA-associated SM-like protein LSM5; SM fold,	99.92
2y9a_D	126	Small nuclear ribonucleoprotein SM D3; splicing-RN	99.92
1b34_A	119	Protein (small nuclear ribonucleoprotein SM D1); s	99.91
4emg_A	93	Probable U6 snRNA-associated SM-like protein LSM3;	99.91
1d3b_B	91	Protein (small nuclear ribonucleoprotein associat	99.91
2fwk_A	121	U6 snRNA-associated SM-like protein LSM5; structur	99.9
3s6n_E	92	Small nuclear ribonucleoprotein E; SMN complex, SM	99.9
4emk_C	113	U6 snRNA-associated SM-like protein LSM7; SM fold,	99.9
1b34_B	118	Protein (small nuclear ribonucleoprotein SM D2); s	99.87
3pgw_B	231	SM B; protein-RNA complex, U1 snRNA, SM fold, SM c	99.85
1m5q_A	130	SMAP3, small nuclear ribonucleoprotein homolog, SM	99.85
1y96_A	86	Gemin6, SIP2, GEM-associated protein 6; SM fold, p	99.23
2vxe_A	88	CG10686-PA; EDC3, CAR-1, P-bodies, decapping, mRNA	97.35
2ylb_A	74	Protein HFQ; RNA-binding protein, LSM protein, RNA	97.35
1u1s_A	82	HFQ protein; SM-like bacterial protein, riken stru	97.27
3sb2_A	79	Protein HFQ; SM-like, RNA chaperone, chaperone; 2.	97.27
3ahu_A	78	Protein HFQ; SM-like motif, protein-RNA complex, t	97.18
2y90_A	104	Protein HFQ; RNA-binding protein, SM-like, RNA cha	97.09
3hfo_A	70	SSR3341 protein; HFQ, SM, RNA-binding protein, sRN	97.08
3hfn_A	72	ASL2047 protein; HFQ, SM, RNA-binding protein, sRN	96.98
1kq1_A	77	HFQ, HOST factor for Q beta; hexamer, RNA binding	96.96
4a53_A	125	EDC3; RNA binding protein; NMR {Schizosaccharomyce	96.88
2fb7_A	95	SM-like protein, LSM-14_N (RAP55); DR.13312, BC055	96.79
2vc8_A	84	Enhancer of mRNA-decapping protein 3; P-BODY compo	96.7
2qtx_A	71	Uncharacterized protein MJ1435; HFQ, SM, RNA-bindi	96.34
1y96_B	85	Gemin7, SIP3, GEM-associated protein 7; SM fold, p	96.26
1ycy_A	71	Conserved hypothetical protein; structural genomic	96.24
1ib8_A	164	Conserved protein SP14.3; nucleic acid binding pro	93.41
3rux_A	270	BIRA bifunctional protein; biotin-protein ligase,	92.3
1sg5_A	86	ORF, hypothetical protein; A+B protein, montreal-k	89.56
1bia_A	321	BIRA bifunctional protein; transcription regulatio	89.45
2eay_A	233	Biotin [acetyl-COA-carboxylase] ligase; biotin bio	89.41
2ej9_A	237	Putative biotin ligase; biotin biosynthesis, monom	88.36
2xk0_A	69	Polycomb protein PCL; transcription, aromatic CAGE	86.49
2rm4_A	103	CG6311-PB, DM EDC3; enhancer of mRNA decapping, P-	86.34
2e12_A	101	SM-like motif, hypothetical protein XCC3642; novel	81.01

>3s6n_F Small nuclear ribonucleoprotein F; SMN complex, SMN-gemin2 complex, U-rich snRNA, SM fold, SM C SNRNPS, snRNP biogenesis, PRE-mRNA splicing; 2.50A {Homo sapiens} PDB: 2y9b_F 2y9c_F 2y9d_F 3cw1_F 3pgw_F* 2y9a_F

Probab=100.00  E-value=1.5e-32  Score=169.78  Aligned_cols=86  Identities=77%  Similarity=1.226  Sum_probs=71.6

Q ss_pred             CCCCCCCCcHHHHhhcCCCEEEEEEcCccEEEEEEEEecCCcceEEcceEEEecCeeeeeeceEEEeCCcEEEEEcCCCC
Q psy6372           1 MSTPLPCNPKPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTGKLGEVLIRCNNILYIRGAEEG   80 (88)
Q Consensus         1 m~~~~~~~p~~~L~~~i~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~d~~e~~~~~~~~~~~~v~IrG~~I~~I~~~d~~   80 (88)
                      ||  .|..|++||++++|++|+|+|+||+.|+|+|.+||+|||++|+||.+..+++..+.++.++|||++|+||.++|++
T Consensus         1 ms--~~~~P~~~L~~~~~k~V~V~Lk~g~~~~G~L~~~D~~mNlvL~d~~e~~~g~~~~~lg~v~IRG~nI~~i~~~d~~   78 (86)
T 3s6n_F            1 MS--LPLNPKPFLNGLTGKPVMVKLKWGMEYKGYLVSVDGYMNMQLANTEEYIDGALSGHLGEVLIRCNNVLYIRGVEEE   78 (86)
T ss_dssp             ----CCCCHHHHHHHHTTSEEEEEETTSCEEEEEEEEECTTCCEEEEEEEEEETTEEEEEESSEEECGGGEEEEEECC--
T ss_pred             CC--cCcCcHHHHHHhCCCeEEEEEcCCeEEEEEEEEEcCceEEEEeeEEEEcCCceeeEccEEEEeCCeEEEEEeCCcc
Confidence            55  5889999999999999999999999999999999999999999999988887789999999999999999999999


Q ss_pred             CccccccC
Q psy6372          81 DEEGEMRE   88 (88)
Q Consensus        81 ~~~~~~~~   88 (88)
                      +++|+|||
T Consensus        79 ~~~~~~~~   86 (86)
T 3s6n_F           79 EEDGEMRE   86 (86)
T ss_dssp             --------
T ss_pred             cccccccC
Confidence            99999997

>1i4k_A Putative snRNP SM-like protein; core snRNP domain, RNA binding protein; HET: CIT; 2.50A {Archaeoglobus fulgidus} SCOP: b.38.1.1 PDB: 1i5l_A*

Probab=99.95  E-value=6.7e-27  Score=141.07  Aligned_cols=75  Identities=35%  Similarity=0.507  Sum_probs=69.6

Q ss_pred             CCcHHHHhhcCCCEEEEEEcCccEEEEEEEEecCCcceEEcceEEEecCeeeeeeceEEEeCCcEEEEEcCCCCC
Q psy6372           7 CNPKPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTGKLGEVLIRCNNILYIRGAEEGD   81 (88)
Q Consensus         7 ~~p~~~L~~~i~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~d~~e~~~~~~~~~~~~v~IrG~~I~~I~~~d~~~   81 (88)
                      ..|+++|++++|++|+|+|+||+.|+|+|.+||+|||++|+||.++..+...+.++.++|||++|++|.++|+.|
T Consensus         3 ~~P~~~L~~~~~~~V~V~L~~g~~~~G~L~~~D~~mNlvL~d~~e~~~~~~~~~lg~v~iRG~~I~~i~~~d~~~   77 (77)
T 1i4k_A            3 PRPLDVLNRSLKSPVIVRLKGGREFRGTLDGYDIHMNLVLLDAEEIQNGEVVRKVGSVVIRGDTVVFVSPAPGGE   77 (77)
T ss_dssp             CCHHHHHHTTTTSEEEEEETTSCEEEEEEEEECTTCCEEEEEEEEEETTEEEEEEEEEEECGGGEEEEEECC---
T ss_pred             ccHHHHHHHhCCCEEEEEEcCCCEEEEEEEEEcCCCCeEEeeEEEEecCCcEeECCEEEECCCEEEEEEeCCCCC
Confidence            479999999999999999999999999999999999999999999988888899999999999999999998753

>1d3b_A Protein (small nuclear ribonucleoprotein SM D3); snRNP, splicing, core snRNP domain, systemic lupus eryth SLE, RNA binding protein; HET: CIT; 2.00A {Homo sapiens} SCOP: b.38.1.1

Probab=99.94  E-value=6.9e-27  Score=141.00  Aligned_cols=73  Identities=25%  Similarity=0.398  Sum_probs=68.3

Q ss_pred             CCCcHHHHhhcCCCEEEEEEcCccEEEEEEEEecCCcceEEcceEEEecCeeeeeeceEEEeCCcEEEEEcCC
Q psy6372           6 PCNPKPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTGKLGEVLIRCNNILYIRGAE   78 (88)
Q Consensus         6 ~~~p~~~L~~~i~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~d~~e~~~~~~~~~~~~v~IrG~~I~~I~~~d   78 (88)
                      ...|++||++++|++|+|+|++|++|+|+|.+||+|||++|+||+++..++..++++.+||||++|+||++||
T Consensus         3 ~~~P~~~L~~~~g~~V~VeLk~g~~~~G~L~~~D~~MNl~L~~~~e~~~~~~~~~lg~v~IRG~nI~~i~lPd   75 (75)
T 1d3b_A            3 IGVPIKVLHEAEGHIVTCETNTGEVYRGKLIEAEDNMNCQMSNITVTYRDGRVAQLEQVYIRGCKIRFLILPD   75 (75)
T ss_dssp             -CCHHHHHHHTTTSEEEEEETTSCEEEEEEEEECTTCCEEEEEEEEECTTSCEEEEEEEEECGGGEEEEEECC
T ss_pred             ccCHHHHHHHhCCCEEEEEECCCcEEEEEEEEEccceeEEEEeEEEECCCCcEEEcCeEEEeCCEEEEEEcCC
Confidence            3679999999999999999999999999999999999999999999965556899999999999999999997

>1h64_1 SnRNP SM-like protein; SM fold, spliceosome, snRNP core; 1.9A {Pyrococcus abyssi} SCOP: b.38.1.1 PDB: 1m8v_A*

Probab=99.94  E-value=1.1e-26  Score=139.66  Aligned_cols=73  Identities=34%  Similarity=0.493  Sum_probs=68.6

Q ss_pred             CCcHHHHhhcCCCEEEEEEcCccEEEEEEEEecCCcceEEcceEEEecCeeeeeeceEEEeCCcEEEEEcCCC
Q psy6372           7 CNPKPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTGKLGEVLIRCNNILYIRGAEE   79 (88)
Q Consensus         7 ~~p~~~L~~~i~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~d~~e~~~~~~~~~~~~v~IrG~~I~~I~~~d~   79 (88)
                      ..|+++|++++|++|+|+|+||+.|+|+|.+||+|||++|+||.++..+...+.+|.++|||++|++|.++||
T Consensus         3 ~~P~~~L~~~~~~~V~V~l~~g~~~~G~L~~~D~~mNlvL~d~~e~~~~~~~~~lg~v~iRG~~I~~i~~~~e   75 (75)
T 1h64_1            3 ERPLDVIHRSLDKDVLVILKKGFEFRGRLIGYDIHLNVVLADAEMIQDGEVVKRYGKIVIRGDNVLAISPTEE   75 (75)
T ss_dssp             CCHHHHHHTTTTSEEEEEETTSEEEEEEEEEECTTCCEEEEEEEEEETTEEEEEEEEEEECGGGEEEEEEC--
T ss_pred             chHHHHHHHHCCCEEEEEECCCCEEEEEEEEEeCCCCeEEeeEEEEeeCCceeECCEEEECCCEEEEEEeCCC
Confidence            4799999999999999999999999999999999999999999999888888999999999999999999875

>1th7_A SnRNP-2, small nuclear riboprotein protein; archaea, SM protein, SM fold, SS-SM1, RNA binding protein; 1.68A {Sulfolobus solfataricus} SCOP: b.38.1.1

Probab=99.94  E-value=1.1e-26  Score=141.66  Aligned_cols=77  Identities=31%  Similarity=0.372  Sum_probs=70.7

Q ss_pred             CCCCCCcHHHHhhcCCCEEEEEEcCccEEEEEEEEecCCcceEEcceEEEecCeeeeeeceEEEeCCcEEEEEcCCC
Q psy6372           3 TPLPCNPKPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTGKLGEVLIRCNNILYIRGAEE   79 (88)
Q Consensus         3 ~~~~~~p~~~L~~~i~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~d~~e~~~~~~~~~~~~v~IrG~~I~~I~~~d~   79 (88)
                      +..+..|+++|++++|++|+|+|+||+.|+|+|.+||+|||++|+||.|+..+...+.+|.++|||++|++|.++|+
T Consensus         4 ~~~~~~P~~~L~~~~~~~V~V~l~~g~~~~G~L~~~D~~mNlvL~d~~e~~~~~~~~~lg~v~iRG~~I~~i~~~~~   80 (81)
T 1th7_A            4 NFLAETAHKVLAESLNNLVLVKLKGNKEVRGMLRSYDQHMNLVLSDSEEIQSDGSGKKLGTIVIRGDNVILISPLQT   80 (81)
T ss_dssp             CTTCHHHHHHHHHHTTSEEEEEETTTEEEEEEEEEECTTCCEEEEEEEEECSSSCEEEEEEEEECGGGEEEEEEC--
T ss_pred             cccccchHHHHHHhCCCeEEEEEcCCcEEEEEEEEEcCCCCEEEccEEEEecCCceeECCEEEECCCEEEEEEecCC
Confidence            44468899999999999999999999999999999999999999999999777778999999999999999999874

>4emk_B U6 snRNA-associated SM-like protein LSM6; SM fold, mRNA decay and PRE-mRNA splicing, LSM proteins, RNA protein; 2.30A {Schizosaccharomyces pombe} PDB: 3swn_B

Probab=99.94  E-value=9.9e-27  Score=140.08  Aligned_cols=73  Identities=44%  Similarity=0.773  Sum_probs=68.5

Q ss_pred             CCcHHHHhhcCCCEEEEEEcCccEEEEEEEEecCCcceEEcceEEEecCeeeeeeceEEEeCCcEEEEEcCCC
Q psy6372           7 CNPKPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTGKLGEVLIRCNNILYIRGAEE   79 (88)
Q Consensus         7 ~~p~~~L~~~i~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~d~~e~~~~~~~~~~~~v~IrG~~I~~I~~~d~   79 (88)
                      ..|+++|++++|++|+|+|+||++|+|+|.+||+|||++|+||.+..+++..+++|.++|||++|+||++.|+
T Consensus         3 ~~P~~~L~~~~~k~V~V~Lk~g~~~~G~L~~~D~~mNlvL~d~~e~~~~~~~~~lg~v~iRG~~I~~i~~~~~   75 (75)
T 4emk_B            3 SSPNEFLNKVIGKKVLIRLSSGVDYKGILSCLDGYMNLALERTEEYVNGKKTNVYGDAFIRGNNVLYVSALDD   75 (75)
T ss_dssp             SHHHHHHHHTTTSEEEEECTTSCEEEEEEEEECTTCEEEEEEEEEEETTEEEEEEEEEEEEGGGSSEEEEC--
T ss_pred             CchHHHHHHhCCCeEEEEEcCCcEEEEEEEEEcCcceEEEccEEEEecCCcccEecEEEEcCCeEEEEEecCC
Confidence            6899999999999999999999999999999999999999999999888788999999999999999998764

>1ljo_A Archaeal SM-like protein AF-SM2; snRNP, core snRNP domain, RNA binding protein, unknown F; 1.95A {Archaeoglobus fulgidus} SCOP: b.38.1.1

Probab=99.94  E-value=3.3e-26  Score=138.18  Aligned_cols=73  Identities=29%  Similarity=0.437  Sum_probs=68.6

Q ss_pred             CCcHHHHhhcCCCEEEEEEcCc-cEEEEEEEEecCCcceEEcceEEEecCeeeeeeceEEEeCCcEEEEEcCCC
Q psy6372           7 CNPKPFLNLLTGKSVICKLKWG-HEYKGILVSTDGYMNCQLASTEEIIDGHCTGKLGEVLIRCNNILYIRGAEE   79 (88)
Q Consensus         7 ~~p~~~L~~~i~k~V~V~L~~g-~~~~G~L~~~D~~mNlvL~d~~e~~~~~~~~~~~~v~IrG~~I~~I~~~d~   79 (88)
                      ..|+++|++++|++|+|+|++| ++|+|+|.+||+|||++|+||.|+..++..+.+|.++|||++|++|.++|+
T Consensus         4 ~~P~~~L~~~~~~~v~V~lk~g~~~~~G~L~~~D~~mNlvL~d~~e~~~~~~~~~lg~v~iRG~nI~~i~~~de   77 (77)
T 1ljo_A            4 VLPNQMVKSMVGKIIRVEMKGEENQLVGKLEGVDDYMNLYLTNAMECKGEEKVRSLGEIVLRGNNVVLIQPQEE   77 (77)
T ss_dssp             CCHHHHHHHTTTSEEEEEETTCSSEEEEEEEEECTTCCEEEEEEEEEETTEEEEEEEEEEECGGGEEEEEEC--
T ss_pred             cchHHHHHHHCCCEEEEEEeCCCEEEEEEEEEECCcceEEEeeEEEEecCCcEeECCeEEEeCCeEEEEEeCCC
Confidence            3799999999999999999999 999999999999999999999999888889999999999999999999885

>1i8f_A Putative snRNP SM-like protein; beta barrel-like SMAP monomers form 35-stranded beta-sheet I heptamer, structural genomics; 1.75A {Pyrobaculum aerophilum} SCOP: b.38.1.1 PDB: 1lnx_A*

Probab=99.94  E-value=2.4e-26  Score=140.19  Aligned_cols=74  Identities=32%  Similarity=0.351  Sum_probs=68.3

Q ss_pred             CCCCcHHHHhhcCCCEEEEEEcCccEEEEEEEEecCCcceEEcceEEEecCeeeeeeceEEEeCCcEEEEEcCCC
Q psy6372           5 LPCNPKPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTGKLGEVLIRCNNILYIRGAEE   79 (88)
Q Consensus         5 ~~~~p~~~L~~~i~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~d~~e~~~~~~~~~~~~v~IrG~~I~~I~~~d~   79 (88)
                      .+..|+.+|.+++|++|+|+|+||+.|.|+|.+||+|||++|+||.|+ ++...+.++.++|||++|++|.++|.
T Consensus         8 ~~~~P~~~L~~~~~~~V~V~l~~g~~~~G~L~~~D~~mNlvL~d~~e~-~~~~~~~lg~v~iRG~~I~~i~~~dg   81 (81)
T 1i8f_A            8 CFATLGATLQDSIGKQVLVKLRDSHEIRGILRSFDQHVNLLLEDAEEI-IDGNVYKRGTMVVRGENVLFISPVPG   81 (81)
T ss_dssp             --CCHHHHHHTTTTSEEEEEEGGGEEEEEEEEEECTTCCEEEEEEEEE-ETTEEEEEEEEEECGGGEEEEEECC-
T ss_pred             cccchHHHHHHHCCCeEEEEEcCCcEEEEEEEEEcCCCeeEEccEEEE-cCCcccCCCEEEECCCEEEEEEeCCC
Confidence            468999999999999999999999999999999999999999999999 66678999999999999999998873

>4emh_A Probable U6 snRNA-associated SM-like protein LSM4; SM fold, mRNA decay, PRE-mRNA splicing, LSM proteins, RNA BI protein; 2.20A {Schizosaccharomyces pombe}

Probab=99.93  E-value=3.2e-26  Score=146.14  Aligned_cols=80  Identities=34%  Similarity=0.471  Sum_probs=56.0

Q ss_pred             CCCCCCcHHHHhhcCCCEEEEEEcCccEEEEEEEEecCCcceEEcceEEEe-cCeeeeeeceEEEeCCcEEEEEcCCCCC
Q psy6372           3 TPLPCNPKPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEII-DGHCTGKLGEVLIRCNNILYIRGAEEGD   81 (88)
Q Consensus         3 ~~~~~~p~~~L~~~i~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~d~~e~~-~~~~~~~~~~v~IrG~~I~~I~~~d~~~   81 (88)
                      |.-|..|+.||++++|++|+|+|++|++|+|+|.+||+|||++|+||++.. +++..+.++.++|||++|+||.+||+..
T Consensus        11 ~~~~~~p~~lL~~~igk~V~V~Lk~G~~~~G~L~~~D~~MNlvL~d~~e~~~dg~~~~~lg~v~IRG~nI~~I~~pd~l~   90 (105)
T 4emh_A           11 SQDPMLPLTLLNATQGRPILVELKNGETFNGHLENCDNYMNLTLREVIRTMPDGDKFFRLPECYIRGNNIKYLRIQDEVL   90 (105)
T ss_dssp             ---------------CCEEEEEETTSCEEEEEEEEECTTCCEEEEEEEEECTTSCEEEEEEEEEECGGGEEEEEC-----
T ss_pred             cCCCCcHHHHHHHhCCCEEEEEECCCCEEEEEEEEEcCCceEEEEEEEEEccCCceeeEcCeEEEeCCeEEEEecCHHHh
Confidence            456889999999999999999999999999999999999999999999984 5556889999999999999999999876


Q ss_pred             c
Q psy6372          82 E   82 (88)
Q Consensus        82 ~   82 (88)
                      +
T Consensus        91 d   91 (105)
T 4emh_A           91 S   91 (105)
T ss_dssp             -
T ss_pred             h
Confidence            4

>1n9r_A SMF, small nuclear ribonucleoprotein F, snRNP-F, SM protein F; heptamer, translation; 2.80A {Saccharomyces cerevisiae} SCOP: b.38.1.1 PDB: 1n9s_A

Probab=99.93  E-value=4.5e-26  Score=142.60  Aligned_cols=77  Identities=52%  Similarity=0.861  Sum_probs=64.5

Q ss_pred             CCCCCCcHHHHhhcCCCEEEEEEcCc-cEEEEEEEEecCCcceEEcceEEEecCeeeeeeceEEEeCCcEEEEEcCCC
Q psy6372           3 TPLPCNPKPFLNLLTGKSVICKLKWG-HEYKGILVSTDGYMNCQLASTEEIIDGHCTGKLGEVLIRCNNILYIRGAEE   79 (88)
Q Consensus         3 ~~~~~~p~~~L~~~i~k~V~V~L~~g-~~~~G~L~~~D~~mNlvL~d~~e~~~~~~~~~~~~v~IrG~~I~~I~~~d~   79 (88)
                      ...+..|+++|++++|++|+|+|+|| ++|+|+|.+||+|||++|+||+++.+++..+.+|.++|||++|+||.++++
T Consensus        16 ~~~~~~P~~~L~~~i~k~V~V~Lk~g~~~~~G~L~~~D~~MNlvL~d~~E~~~~~~~~~lg~v~IRG~nI~~I~~~~~   93 (93)
T 1n9r_A           16 AMQPVNPKPFLKGLVNHRVGVKLKFNSTEYRGTLVSTDNYFNLQLNEAEEFVAGVSHGTLGEIFIRCNNVLYIRELPN   93 (93)
T ss_dssp             ----------CGGGTTSEEEEEESSTTEEEEEEEEECCTTTCEEEEEEEEEETTEEEEECCSEEECGGGEEEEEECCC
T ss_pred             ccccCChHHHHHHhCCCEEEEEEcCCCEEEEEEEEEEccccEEEEeeEEEEcCCCeEeEcCEEEEcCCeEEEEEeCCC
Confidence            45678899999999999999999999 999999999999999999999999888888999999999999999998874

>1mgq_A SM-like protein; LSM, RNA-binding, archea, RNA binding protein; 1.70A {Methanothermobacterthermautotrophicus} SCOP: b.38.1.1 PDB: 1i81_A 1loj_A* 1jbm_A 1jri_A

Probab=99.93  E-value=2.8e-25  Score=136.05  Aligned_cols=73  Identities=41%  Similarity=0.490  Sum_probs=69.1

Q ss_pred             CCCCCcHHHHhhcCCCEEEEEEcCccEEEEEEEEecCCcceEEcceEEEecCeeeeeeceEEEeCCcEEEEEc
Q psy6372           4 PLPCNPKPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTGKLGEVLIRCNNILYIRG   76 (88)
Q Consensus         4 ~~~~~p~~~L~~~i~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~d~~e~~~~~~~~~~~~v~IrG~~I~~I~~   76 (88)
                      .++..|+.+|++++|++|+|+|+||+.|+|+|.+||+|||++|+||.|+..+...+.+|.++|||++|++|++
T Consensus        11 ~~~~~P~~~L~~~~~~~V~V~Lk~g~~~~G~L~~~D~~mNlvL~d~~e~~~~~~~~~lg~v~IRG~~I~~i~p   83 (83)
T 1mgq_A           11 VNVQRPLDALGNSLNSPVIIKLKGDREFRGVLKSFDLHMNLVLNDAEELEDGEVTRRLGTVLIRGDNIVYISP   83 (83)
T ss_dssp             CCTTCTTHHHHHTTTSEEEEEETTTEEEEEEEEEECTTCCEEEEEEEEEETTEEEEEEEEEEECGGGEEEEEC
T ss_pred             ccCcChHHHHHHhCCCEEEEEEcCCcEEEEEEEEECCCceeEEccEEEEecCCcccCCCEEEECCCEEEEEEC
Confidence            4567899999999999999999999999999999999999999999999888889999999999999999974

>3s6n_G Small nuclear ribonucleoprotein G; SMN complex, SMN-gemin2 complex, U-rich snRNA, SM fold, SM C SNRNPS, snRNP biogenesis, PRE-mRNA splicing; 2.50A {Homo sapiens} PDB: 2y9b_G 2y9c_G 2y9d_G 3cw1_G 3pgw_G* 2y9a_G

Probab=99.92  E-value=2.2e-25  Score=134.52  Aligned_cols=71  Identities=28%  Similarity=0.398  Sum_probs=53.5

Q ss_pred             cHHHHhhcCCCEEEEEEcCccEEEEEEEEecCCcceEEcceEEEecCeeeeeeceEEEeCCcEEEEEcCCC
Q psy6372           9 PKPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTGKLGEVLIRCNNILYIRGAEE   79 (88)
Q Consensus         9 p~~~L~~~i~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~d~~e~~~~~~~~~~~~v~IrG~~I~~I~~~d~   79 (88)
                      |.++|++++|++|+|+|+||+.|+|+|.+||+|||++|+||.|+..++..+.+|.++|||++|++|++.|.
T Consensus         5 ~~~~L~~~~~k~V~V~Lk~gr~~~G~L~~~D~~mNlvL~~~~e~~~~~~~~~lg~v~iRG~~I~~i~~~d~   75 (76)
T 3s6n_G            5 HPPELKKFMDKKLSLKLNGGRHVQGILRGFDPFMNLVIDECVEMATSGQQNNIGMVVIRGNSIIMLEALER   75 (76)
T ss_dssp             ---------CCEEEEEETTTEEEEEEEEEECTTCCEEEEEEEECCCC----CBSSEEECSSSEEEEEC---
T ss_pred             chHHHHHhCCCeEEEEECCCcEEEEEEEEECCcceEEEeceEEEccCCcEeEcCEEEECCCeEEEEEeccC
Confidence            67899999999999999999999999999999999999999998766678999999999999999998874

>3bw1_A SMX4 protein, U6 snRNA-associated SM-like protein LSM3; RNA-binding protein, SM protein, ring, HOMO octamer, mRNA processing; 2.50A {Saccharomyces cerevisiae}

Probab=99.92  E-value=1e-24  Score=136.91  Aligned_cols=77  Identities=25%  Similarity=0.279  Sum_probs=67.2

Q ss_pred             CCcHHHHhhcCCCEEEEEEcCccEEEEEEEEecCCcceEEcceEEEec-------CeeeeeeceEEEeCCcEEEEEcCCC
Q psy6372           7 CNPKPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIID-------GHCTGKLGEVLIRCNNILYIRGAEE   79 (88)
Q Consensus         7 ~~p~~~L~~~i~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~d~~e~~~-------~~~~~~~~~v~IrG~~I~~I~~~d~   79 (88)
                      ..|+.+|.+++|++|+|+|++|+.|.|+|.+||+|||++|+||.|.+.       +...+.+|.++|||++|++|.++++
T Consensus         9 ~~p~~~L~~~i~k~V~V~Lk~gr~~~G~L~~fD~~mNlVL~d~~E~~~~~~~~~~~~~~r~lG~v~IRG~nVv~I~~~d~   88 (96)
T 3bw1_A            9 ETPLDLLKLNLDERVYIKLRGARTLVGTLQAFDSHCNIVLSDAVETIYQLNNEELSESERRCEMVFIRGDTVTLISTPSE   88 (96)
T ss_dssp             CCHHHHHGGGTTSEEEEEEGGGCEEEEEEEEECTTCCEEEEEEEEEEECCSTTCCCEEEEEEEEEEECGGGEEEEECCC-
T ss_pred             hhHHHHHHHHCCCeEEEEECCCcEEEEEEEEECCCCcEEEcCEEEEeccccccccCcceeEcCEEEECCCEEEEEEecCc
Confidence            579999999999999999999999999999999999999999999853       3467899999999999999999888


Q ss_pred             CCcc
Q psy6372          80 GDEE   83 (88)
Q Consensus        80 ~~~~   83 (88)
                      ++|.
T Consensus        89 ~~d~   92 (96)
T 3bw1_A           89 DDDG   92 (96)
T ss_dssp             ----
T ss_pred             cccc
Confidence            7553

>4emk_A U6 snRNA-associated SM-like protein LSM5; SM fold, mRNA decay and PRE-mRNA splicing, LSM proteins, RNA protein; 2.30A {Schizosaccharomyces pombe} PDB: 3swn_A

Probab=99.92  E-value=1.7e-24  Score=135.73  Aligned_cols=74  Identities=23%  Similarity=0.293  Sum_probs=67.1

Q ss_pred             CCCCcHHHHhhcCCCEEEEEEcCccEEEEEEEEecCCcceEEcceEEEe-cCeeeeeeceEEEeCCcEEEEEcCC
Q psy6372           5 LPCNPKPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEII-DGHCTGKLGEVLIRCNNILYIRGAE   78 (88)
Q Consensus         5 ~~~~p~~~L~~~i~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~d~~e~~-~~~~~~~~~~v~IrG~~I~~I~~~d   78 (88)
                      ....|+.+|.+++|++|+|+|++|+.|+|+|.+||+|||++|+||+|+. +++..+.+|.++|||++|++|.+..
T Consensus        17 ~~~~Pl~lL~~~l~k~V~V~Lk~gr~~~G~L~gfD~~mNlvL~d~~E~~~~~~~~~~lg~v~IRG~nI~~i~p~~   91 (94)
T 4emk_A           17 MTILPLELIDKCIGSNLWVIMKSEREFAGTLVGFDDYVNIVLKDVTEYDTVTGVTEKHSEMLLNGNGMCMLIPGG   91 (94)
T ss_dssp             ---CHHHHHHHTTTSEEEEEESSSEEEEEEEEEECTTCCEEEEEEEEEETTTCCEEEEEEEEECSTTEEEEEECC
T ss_pred             ccccCHHHHHHHcCCeEEEEECCCcEEEEEEEEEcccCCeEeeeEEEEecCCCcEeEcCEEEEcCCEEEEEEeCC
Confidence            3467999999999999999999999999999999999999999999997 6667899999999999999999653

>2y9a_D Small nuclear ribonucleoprotein SM D3; splicing-RNA complex, PRE-mRNA splicing, spliceosome, snRNP biogenesis, SM site, SM fold, heteromeric heptameric ring; 3.60A {Homo sapiens} PDB: 2y9b_D 2y9c_D 2y9d_D 3pgw_Z* 3cw1_D

Probab=99.92  E-value=1.2e-24  Score=142.66  Aligned_cols=77  Identities=23%  Similarity=0.368  Sum_probs=70.2

Q ss_pred             CCCcHHHHhhcCCCEEEEEEcCccEEEEEEEEecCCcceEEcceEEEecCeeeeeeceEEEeCCcEEEEEcCCCCCc
Q psy6372           6 PCNPKPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTGKLGEVLIRCNNILYIRGAEEGDE   82 (88)
Q Consensus         6 ~~~p~~~L~~~i~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~d~~e~~~~~~~~~~~~v~IrG~~I~~I~~~d~~~~   82 (88)
                      ...|+.||++++|++|+|+|+||++|+|+|.+||+|||++|+||+++..+....+++.+||||++|+||++||+...
T Consensus         3 ~~~P~~~L~~~~gk~V~VeLknG~~~~G~L~~~D~~MNi~L~dv~e~~~~g~~~~l~~v~IRGnnI~~I~lpd~l~~   79 (126)
T 2y9a_D            3 IGVPIKVLHEAEGHIVTCETNTGEVYRGKLIEAEDNMNCQMSNITVTYRDGRVAQLEQVYIRGSKIRFLILPDMLKN   79 (126)
T ss_dssp             -CCSHHHHHSCSSCEEEEEESSCCEEEEEEEEECTTSCEEEEEEEEECTTSCCEEEEEEEECGGGEEEEECCSSCSS
T ss_pred             cccHHHHHHHhCCCEEEEEECCCcEEEEEEEEEcCceEEEEeeEEEEcCCCcEeecccEEEeCCEEEEEEccccccc
Confidence            36899999999999999999999999999999999999999999998644458899999999999999999987643

>1b34_A Protein (small nuclear ribonucleoprotein SM D1); snRNP, splicing, spliceosome, core snRNP domain, systemi erythematosus, SLE, RNA binding protein; 2.50A {Homo sapiens} SCOP: b.38.1.1 PDB: 2y9a_B 2y9b_B 2y9c_B 2y9d_B 3cw1_B 3pgw_X* 3s6n_A

Probab=99.91  E-value=1.8e-24  Score=140.47  Aligned_cols=73  Identities=26%  Similarity=0.292  Sum_probs=69.0

Q ss_pred             CcHHHHhhcCCCEEEEEEcCccEEEEEEEEecCCcceEEcceEEEecCeeeeeeceEEEeCCcEEEEEcCCCC
Q psy6372           8 NPKPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTGKLGEVLIRCNNILYIRGAEEG   80 (88)
Q Consensus         8 ~p~~~L~~~i~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~d~~e~~~~~~~~~~~~v~IrG~~I~~I~~~d~~   80 (88)
                      .|+.||++++|++|+|+|+||++|.|+|.+||+|||++|+||+|+..+.....++.+||||++|+||.+||+-
T Consensus         2 ~p~~~L~~~~gk~V~V~Lk~g~~~~G~L~~~D~~MNlvL~d~~e~~~~~~~~~lg~v~IRG~nI~~I~~pd~l   74 (119)
T 1b34_A            2 KLVRFLMKLSHETVTIELKNGTQVHGTITGVDVSMNTHLKAVKMTLKNREPVQLETLSIRGNNIRYFILPDSL   74 (119)
T ss_dssp             CHHHHHHTCTTCEEEEEETTCCEEEEEEEEECTTCCEEEEEEEEECTTSCCEEEEEEEECGGGEEEEECCTTC
T ss_pred             ChHHHHHHhCCCEEEEEEcCCCEEEEEEEEEcccceEEeccEEEecCCCceeEcceEEEcCCeEEEEEecccc
Confidence            5899999999999999999999999999999999999999999997666788999999999999999999873

>4emg_A Probable U6 snRNA-associated SM-like protein LSM3; SM fold, mRNA decay, LSM proteins, RNA binding protein; 2.70A {Schizosaccharomyces pombe}

Probab=99.91  E-value=3.8e-24  Score=133.73  Aligned_cols=78  Identities=22%  Similarity=0.312  Sum_probs=65.4

Q ss_pred             CC-CCCCCCcHHHHhhcCCCEEEEEEcCccEEEEEEEEecCCcceEEcceEEEec-----C--------eeeeeeceEEE
Q psy6372           1 MS-TPLPCNPKPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIID-----G--------HCTGKLGEVLI   66 (88)
Q Consensus         1 m~-~~~~~~p~~~L~~~i~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~d~~e~~~-----~--------~~~~~~~~v~I   66 (88)
                      || +.....|+.+|+.++|++|+|+|++|+.|+|+|.+||+|||++|+||.|++.     +        ...+.+|.++|
T Consensus         1 m~~~~~~~~Pl~lL~~~~~~~V~V~l~~gr~~~G~L~~~D~~mNlvL~d~~E~~~~~~~~~~~~~~~~~~~~r~lG~v~i   80 (93)
T 4emg_A            1 MESAQAVAEPLDLVRLSLDEIVYVKLRGDRELNGRLHAYDEHLNMVLGDAEEIVTIFDDEETDKDKALKTIRKHYEMLFV   80 (93)
T ss_dssp             --------CTTHHHHTTTTSEEEEEETTTEEEEEEEEEECTTCCEEEEEEEEEEC--------------CEEEEEEEEEE
T ss_pred             CCcccccCCCHHHHHHhCCCEEEEEECCCcEEEEEEEEECCcccEEeecEEEEEeccccCCccccccccccEeEeceEEE
Confidence            44 3456799999999999999999999999999999999999999999999853     2        24789999999


Q ss_pred             eCCcEEEEEcCC
Q psy6372          67 RCNNILYIRGAE   78 (88)
Q Consensus        67 rG~~I~~I~~~d   78 (88)
                      ||++|++|.+|-
T Consensus        81 RG~nVv~I~p~~   92 (93)
T 4emg_A           81 RGDSVILIAPPR   92 (93)
T ss_dssp             CGGGEEEEECCC
T ss_pred             CCCeEEEEEecC
Confidence            999999999863

>1d3b_B Protein (small nuclear ribonucleoprotein associat B); snRNP, splicing, core snRNP domain, systemic lupus eryth SLE, RNA binding protein; HET: CIT; 2.00A {Homo sapiens} SCOP: b.38.1.1 PDB: 2y9a_A 2y9b_A 2y9c_A 2y9d_A

Probab=99.91  E-value=1.2e-24  Score=134.86  Aligned_cols=77  Identities=19%  Similarity=0.214  Sum_probs=65.4

Q ss_pred             CCCcHHHHhhcCCCEEEEEEcCccEEEEEEEEecCCcceEEcceEEEe----------cCeeeeeeceEEEeCCcEEEEE
Q psy6372           6 PCNPKPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEII----------DGHCTGKLGEVLIRCNNILYIR   75 (88)
Q Consensus         6 ~~~p~~~L~~~i~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~d~~e~~----------~~~~~~~~~~v~IrG~~I~~I~   75 (88)
                      |.+|.++|.+++|++|+|+|+||+.|.|+|.+||+|||++|+||.|++          .+...+.+|.++|||++|++|.
T Consensus         2 ~~~~~~~L~~~~~k~V~V~l~~gr~~~G~L~~~D~~mNlvL~d~~E~~~~~~~~~~~~~~~~~~~lg~v~iRG~~I~~i~   81 (91)
T 1d3b_B            2 TVGKSSKMLQHIDYRMRCILQDGRIFIGTFKAFDKHMNLILCDCDEFRKIKPKNSKQAEREEKRVLGLVLLRGENLVSMT   81 (91)
T ss_dssp             -----CCCGGGTTSEEEEEETTCCEEEEEEEECCTTCCEEEEEEEEEEEECCSSTTSCCEEEEEEEEEEEECGGGEEEEE
T ss_pred             CCChhHHHHHHcCCcEEEEECCCeEEEEEEEEECCCCeEEecCEEEEeeccccccccccCccEeECCEEEECCCeEEEEE
Confidence            457889999999999999999999999999999999999999999964          2346889999999999999999


Q ss_pred             cCCCCCc
Q psy6372          76 GAEEGDE   82 (88)
Q Consensus        76 ~~d~~~~   82 (88)
                      +++....
T Consensus        82 ~~~~~~~   88 (91)
T 1d3b_B           82 VEGPPPK   88 (91)
T ss_dssp             EEECCC-
T ss_pred             cCCCCCC
Confidence            8876654

>2fwk_A U6 snRNA-associated SM-like protein LSM5; structural genomics, structural genomics consortium, SGC, DNA binding protein; 2.14A {Cryptosporidium parvum} SCOP: b.38.1.1 PDB: 3pgg_A

Probab=99.90  E-value=3.8e-24  Score=139.19  Aligned_cols=78  Identities=21%  Similarity=0.296  Sum_probs=68.2

Q ss_pred             CCCCcHHHHhhcCCCEEEEEEcCccEEEEEEEEecCCcceEEcceEEEec----------Cee-----eeeeceEEEeCC
Q psy6372           5 LPCNPKPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIID----------GHC-----TGKLGEVLIRCN   69 (88)
Q Consensus         5 ~~~~p~~~L~~~i~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~d~~e~~~----------~~~-----~~~~~~v~IrG~   69 (88)
                      ....|+.+|.++++++|+|+|++|+.|.|+|.+||+||||+|+||+|++.          +..     .+.+|+++|||+
T Consensus        25 ~~~~Pl~lL~~~l~k~V~V~Lk~Gr~~~G~L~~fD~~mNlVL~d~~E~~~~~~~~~~~~~g~~~~~~~~r~lG~v~IRG~  104 (121)
T 2fwk_A           25 NIILPLALIDKCIGNRIYVVMKGDKEFSGVLRGFDEYVNMVLDDVQEYGFKADEEDISGGNKKLKRVMVNRLETILLSGN  104 (121)
T ss_dssp             CCCCHHHHHHHTBTSBCEEEETTTEEECCEEEEECTTCCEEEESCCEEEC---------------CEECCCCSEEEECGG
T ss_pred             cccCcHHHHHHHcCCeEEEEECCCcEEEEEEEEEcccCCeEeceEEEEEeccccccccccCcccccccceEcceEEECCC
Confidence            55799999999999999999999999999999999999999999999862          323     688999999999


Q ss_pred             cEEEEEcCCCCCc
Q psy6372          70 NILYIRGAEEGDE   82 (88)
Q Consensus        70 ~I~~I~~~d~~~~   82 (88)
                      +|++|.+.++.++
T Consensus       105 nVv~I~~~~~~~~  117 (121)
T 2fwk_A          105 NVAMLVPGGDPDS  117 (121)
T ss_dssp             GEEEEESSSCC--
T ss_pred             EEEEEEecCCCCC
Confidence            9999998877654

>3s6n_E Small nuclear ribonucleoprotein E; SMN complex, SMN-gemin2 complex, U-rich snRNA, SM fold, SM C SNRNPS, snRNP biogenesis, PRE-mRNA splicing; 2.50A {Homo sapiens} PDB: 2y9b_E 2y9c_E 2y9d_E 3cw1_E 3pgw_E* 2y9a_E

Probab=99.90  E-value=5.5e-24  Score=132.94  Aligned_cols=76  Identities=18%  Similarity=0.331  Sum_probs=67.9

Q ss_pred             CCCCCcHHHHhhcCCCEEEEEE----cCccEEEEEEEEecCCcceEEcceEEEe-cCeeeeeeceEEEeCCcEEEEEcCC
Q psy6372           4 PLPCNPKPFLNLLTGKSVICKL----KWGHEYKGILVSTDGYMNCQLASTEEII-DGHCTGKLGEVLIRCNNILYIRGAE   78 (88)
Q Consensus         4 ~~~~~p~~~L~~~i~k~V~V~L----~~g~~~~G~L~~~D~~mNlvL~d~~e~~-~~~~~~~~~~v~IrG~~I~~I~~~d   78 (88)
                      +.+..|+++|.++++++|+|++    ++|++|.|+|.+||+|||++|+||.|.. +++..+.+|.++|||++|++|.++|
T Consensus        12 ~~m~~Pl~lL~~~l~~~v~V~l~~~~~~gr~~~G~L~gfD~~mNlvL~d~~E~~~~~~~~~~lg~v~iRG~nV~~i~~~~   91 (92)
T 3s6n_E           12 KVMVQPINLIFRYLQNRSRIQVWLYEQVNMRIEGCIIGFDEYMNLVLDDAEEIHSKTKSRKQLGRIMLKGDNITLLQSVS   91 (92)
T ss_dssp             --CCCHHHHHHHHHHHTCEEEEEESSSCSSEEEEEEEEECTTCCEEEEEEEEECSSSCCEEEEEEEEECGGGEEEEEEC-
T ss_pred             eeccCCHHHHHHHhCCCEEEEEEEEecCCEEEEEEEEEEcCcCcEEEeeeEEEecCCCceeEcCeEEEeCCEEEEEEeCC
Confidence            3478899999999999999999    9999999999999999999999999985 4556889999999999999999876


Q ss_pred             C
Q psy6372          79 E   79 (88)
Q Consensus        79 ~   79 (88)
                      +
T Consensus        92 ~   92 (92)
T 3s6n_E           92 N   92 (92)
T ss_dssp             -
T ss_pred             C
Confidence            3

>4emk_C U6 snRNA-associated SM-like protein LSM7; SM fold, mRNA decay and PRE-mRNA splicing, LSM proteins, RNA protein; 2.30A {Schizosaccharomyces pombe} PDB: 3swn_C

Probab=99.90  E-value=2.5e-23  Score=134.12  Aligned_cols=76  Identities=24%  Similarity=0.304  Sum_probs=57.5

Q ss_pred             CCcHHHHhhcCCCEEEEEEcCccEEEEEEEEecCCcceEEcceEEEecC-------eeeeeeceEEEeCCcEEEEEcCCC
Q psy6372           7 CNPKPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDG-------HCTGKLGEVLIRCNNILYIRGAEE   79 (88)
Q Consensus         7 ~~p~~~L~~~i~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~d~~e~~~~-------~~~~~~~~v~IrG~~I~~I~~~d~   79 (88)
                      ..|...|.+++|++|+|+|++|+.|.|+|.+||+||||+|+||.|++.+       ...+.+|.++|||++|++|.++|.
T Consensus        22 ke~i~~L~~~l~k~V~V~L~dGr~~~G~L~~fD~~mNLVL~d~~E~~~~~~~~~~~~~~r~lG~v~IRG~nIv~I~~~d~  101 (113)
T 4emk_C           22 KESILDLSRYQDQRIQATFTGGRQITGILKGFDQLMNLVLDDVEEQLRNPEDGKLTGAIRKLGLVVVRGTTLVLIAPMDG  101 (113)
T ss_dssp             ----------CCSEEEEEETTSCEEEEEEEEECTTCCEEEEEEEEEC---------CCEEEEEEEEECTTTEEEEEECC-
T ss_pred             cchHHHHHHHcCCcEEEEEeCCeEEEEEEEEEcCcccEEEeeEEEEEcCCCCcccccceeEccEEEECCCeEEEEEecCc
Confidence            3466789999999999999999999999999999999999999998532       357899999999999999999987


Q ss_pred             CCc
Q psy6372          80 GDE   82 (88)
Q Consensus        80 ~~~   82 (88)
                      .+|
T Consensus       102 ~ee  104 (113)
T 4emk_C          102 SEE  104 (113)
T ss_dssp             ---
T ss_pred             ccc
Confidence            775

>1b34_B Protein (small nuclear ribonucleoprotein SM D2); snRNP, splicing, spliceosome, core snRNP domain, systemi erythematosus, SLE, RNA binding protein; 2.50A {Homo sapiens} SCOP: b.38.1.1 PDB: 2y9a_C 2y9b_C 2y9c_C 2y9d_C 3cw1_C 3pgw_Y* 3s6n_B

Probab=99.87  E-value=4.9e-22  Score=128.66  Aligned_cols=75  Identities=12%  Similarity=0.150  Sum_probs=64.4

Q ss_pred             CCCcHHHHhhcC--CCEEEEEEcCccEEEEEEEEecCCcceEEcceEEEecC--------------eeeeeeceEEEeCC
Q psy6372           6 PCNPKPFLNLLT--GKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDG--------------HCTGKLGEVLIRCN   69 (88)
Q Consensus         6 ~~~p~~~L~~~i--~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~d~~e~~~~--------------~~~~~~~~v~IrG~   69 (88)
                      ...|+++|..++  +++|+|+|++|+.|.|+|.+||+|||++|+||.|++..              ...+.+|.+||||+
T Consensus        25 ~~~Pl~lL~~~~~~~k~V~V~Lk~gr~~~G~L~~fD~~mNlvL~d~~E~~~~~~~~~~~~~~~~~~~~~r~lg~v~IRG~  104 (118)
T 1b34_B           25 NTGPLSVLTQSVKNNTQVLINCRNNKKLLGRVKAFDRHCNMVLENVKEMWTEVPKSGKGKKKSKPVNKDRYISKMFLRGD  104 (118)
T ss_dssp             -CCHHHHHHHHHHHTCEEEEEETTSCEEEEEEEEECTTCCEEEEEEEEC-------------------CEEEEEEEECGG
T ss_pred             ccChHHHHHHHhcCCcEEEEEECCCcEEEEEEEEeCCceEEEEeCEEEEEecccccccccccccccccccCcCeEEEcCC
Confidence            458999999999  59999999999999999999999999999999987421              01457999999999


Q ss_pred             cEEEEEcCCCC
Q psy6372          70 NILYIRGAEEG   80 (88)
Q Consensus        70 ~I~~I~~~d~~   80 (88)
                      +|++|.+++..
T Consensus       105 nVv~I~~~~~~  115 (118)
T 1b34_B          105 SVIVVLRNPLI  115 (118)
T ss_dssp             GEEEEEECCCC
T ss_pred             EEEEEEeCchh
Confidence            99999988763

>3pgw_B SM B; protein-RNA complex, U1 snRNA, SM fold, SM core, RRM, splici SNRNPS, splicing factors; HET: DNA; 4.40A {Homo sapiens} PDB: 3cw1_A

Probab=99.85  E-value=4.3e-21  Score=136.19  Aligned_cols=73  Identities=21%  Similarity=0.220  Sum_probs=66.1

Q ss_pred             CCcHHHHhhcCCCEEEEEEcCccEEEEEEEEecCCcceEEcceEEEec----------CeeeeeeceEEEeCCcEEEEEc
Q psy6372           7 CNPKPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIID----------GHCTGKLGEVLIRCNNILYIRG   76 (88)
Q Consensus         7 ~~p~~~L~~~i~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~d~~e~~~----------~~~~~~~~~v~IrG~~I~~I~~   76 (88)
                      .++..+|++++||+|+|+|+|||+|.|+|.+||+||||+|+||+|++.          +++.++++++||||++|++|.+
T Consensus         3 v~k~~kL~klIdKrV~V~LkdGRel~GtLkgFDq~MNLVL~Da~E~~~ik~k~~k~~~~~~~R~LGlV~IRGdnIV~Isv   82 (231)
T 3pgw_B            3 VGKSSKMLQHIDYRMRCILQDGRIFIGTFKAFDKHMNLILCDCDEFRKIKPKNSKQAEREEKRVLGLVLLRGENLVSMTV   82 (231)
T ss_pred             cCchHHHHHhcCCeEEEEECCCcEEEEEEEEEcccccEEecCEEEEEeccCcccccccccceeEeceEEECCCcEEEEEe
Confidence            467899999999999999999999999999999999999999999752          2468899999999999999997


Q ss_pred             CCC
Q psy6372          77 AEE   79 (88)
Q Consensus        77 ~d~   79 (88)
                      .+.
T Consensus        83 e~p   85 (231)
T 3pgw_B           83 EGP   85 (231)
T ss_pred             cCC
Confidence            654

>1m5q_A SMAP3, small nuclear ribonucleoprotein homolog, SM-like P; OB-like fold, B-sheet toroid, 14-MER, cadmium-binding site, translation; 2.00A {Pyrobaculum aerophilum} SCOP: b.38.1.1

Probab=99.85  E-value=3.3e-21  Score=126.89  Aligned_cols=70  Identities=30%  Similarity=0.350  Sum_probs=64.1

Q ss_pred             HHHHhhcCCCEEEEEEcCccEEEEEEEEecCCcceEEcceEEEecCeeeeeeceEEEeCCcEEEEEcCCCCCcc
Q psy6372          10 KPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTGKLGEVLIRCNNILYIRGAEEGDEE   83 (88)
Q Consensus        10 ~~~L~~~i~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~d~~e~~~~~~~~~~~~v~IrG~~I~~I~~~d~~~~~   83 (88)
                      .++|++++|++|+|+|+||+.|+|+|.+||+|||++|+||.+. .   .+.+|.++|||++|++|.++|+..+-
T Consensus         2 ~~~L~~~igk~V~V~Lk~G~~~~G~L~~~D~~MNlvL~d~~E~-~---~~~lg~v~IRG~nI~~I~~~d~~~d~   71 (130)
T 1m5q_A            2 VAELNNLLGREVQVVLSNGEVYKGVLHAVDNQLNIVLANASNK-A---GEKFNRVFIMYRYIVHIDSTERRIDM   71 (130)
T ss_dssp             HHHHHHTTTSEEEEEETTSCEEEEEEEEECTTCCEEEEEEECT-T---CCEEEEEEECGGGEEEEEECCCCCCH
T ss_pred             hhHHHHhCCCeEEEEECCCcEEEEEEEEEcccceeEEeeEEEE-c---CCEeceEEEeCCeEEEEEcCCcccCH
Confidence            4689999999999999999999999999999999999999987 2   36889999999999999999987543

>1y96_A Gemin6, SIP2, GEM-associated protein 6; SM fold, protein complex, RNA binding protein; 2.00A {Homo sapiens}

Probab=99.23  E-value=2.7e-11  Score=74.54  Aligned_cols=69  Identities=23%  Similarity=0.219  Sum_probs=59.2

Q ss_pred             CcHHHHhhcCCCEEEEEEcCccEEEEEEEEec-CCcceEEcceEEEecCeeeeeeceEEEeCCcEEEEEcCCCCCcc
Q psy6372           8 NPKPFLNLLTGKSVICKLKWGHEYKGILVSTD-GYMNCQLASTEEIIDGHCTGKLGEVLIRCNNILYIRGAEEGDEE   83 (88)
Q Consensus         8 ~p~~~L~~~i~k~V~V~L~~g~~~~G~L~~~D-~~mNlvL~d~~e~~~~~~~~~~~~v~IrG~~I~~I~~~d~~~~~   83 (88)
                      .|. .|++++||.|.|+|.||++|+|.|.+|| ...|++|.|+.   .   ...+..++|.|..|..|.+.++.++.
T Consensus         8 ~p~-el~~li~KeV~V~l~dg~~y~G~l~tvDp~s~sIvL~n~~---~---~~~~~~~iI~G~aI~eI~v~~~~~~~   77 (86)
T 1y96_A            8 GPL-EWQDYIYKEVRVTASEKNEYKGWVLTTDPVSANIVLVNFL---E---DGSMSVTGIMGHAVQTVETMNEGDHR   77 (86)
T ss_dssp             CHH-HHHHTTTCEEEEEETTTEEEEEEEEEECTTTCCEEEEEEC---T---TSCEEEEEECGGGEEEEEEEECCCHH
T ss_pred             CHH-HHHhhcCCEEEEEEcCCCEEEEEEEEECCCceEEEEeecc---c---CCeEEEEEEecceEEEEEEecchhHH
Confidence            444 7899999999999999999999999999 88999999992   2   24457899999999999887776654

>2vxe_A CG10686-PA; EDC3, CAR-1, P-bodies, decapping, mRNA decay, LSM proteins, translational repression, transcription; NMR {Drosophila melanogaster}

Probab=97.35  E-value=0.002  Score=39.38  Aligned_cols=66  Identities=20%  Similarity=0.169  Sum_probs=54.3

Q ss_pred             hcCCCEEEEEEcCccEEEEEEEEec-CCcceEEcceEEE-ecC--------eeeeeeceEEEeCCcEEEEEcCCCC
Q psy6372          15 LLTGKSVICKLKWGHEYKGILVSTD-GYMNCQLASTEEI-IDG--------HCTGKLGEVLIRCNNILYIRGAEEG   80 (88)
Q Consensus        15 ~~i~k~V~V~L~~g~~~~G~L~~~D-~~mNlvL~d~~e~-~~~--------~~~~~~~~v~IrG~~I~~I~~~d~~   80 (88)
                      .++|++|.+..+.+-.|.|+|..+| +..-+.|.|+..+ .+|        ....-++.+..||+.|.-+.+-+..
T Consensus        10 ~yIGs~iSLISk~dIRYeGiL~~In~~~sTi~L~nVrsfGTEgR~~~~~ipp~~~vy~yIvFrgsDIKdL~V~~~~   85 (88)
T 2vxe_A           10 PELGSKISLISKADIRYEGRLYTVDPQECTIALSSVRSFGTEDRDTQFQIAPQSQIYDYILFRGSDIKDIRVVNNH   85 (88)
T ss_dssp             CCTTCEEEEEETTTEEEEEEEEEEETTTTEEEEEEEEECCCTTTCCSSCCCCCCSCEEEEEEETTTEEEEEECCCC
T ss_pred             cccCCeEEEEECCCceEEEEEeeecCcccEEEEEeeeEecCcCCCCCcccCCCCceeeEEEEccCCccEEEEeccC
Confidence            4799999999999999999999999 5678999999875 221        1344678999999999999877654

>2ylb_A Protein HFQ; RNA-binding protein, LSM protein, RNA chaperone; 1.15A {Salmonella enterica subsp} PDB: 2yht_A 1hk9_A 2ylc_A* 3gib_A* 3rer_A* 3qo3_A* 3res_A*

Probab=97.35  E-value=0.0004  Score=41.26  Aligned_cols=57  Identities=25%  Similarity=0.271  Sum_probs=44.5

Q ss_pred             cHHHHhhcC--CCEEEEEEcCccEEEEEEEEecCCcceEEcceEEEecCeeeeeeceEEEeCCcEEEEEcCC
Q psy6372           9 PKPFLNLLT--GKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTGKLGEVLIRCNNILYIRGAE   78 (88)
Q Consensus         9 p~~~L~~~i--~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~d~~e~~~~~~~~~~~~v~IrG~~I~~I~~~d   78 (88)
                      =-.||+.+.  +.+|+|.|.||..++|++.+||+|+ +.|++.            ...+|.=..|.+|.+..
T Consensus        10 Qd~~L~~lrk~k~~Vti~L~nG~~l~G~I~~fD~f~-vlL~~~------------~~~LIYKhAIsTI~p~~   68 (74)
T 2ylb_A           10 QDPFLNALRRERVPVSIYLVNGIKLQGQIESFDQFV-ILLKNT------------VSQMVYKHAISTVVPSR   68 (74)
T ss_dssp             HHHHHHHHHHHTCCEEEEETTSCEEEEEEEEECSSE-EEEESS------------SEEEEEGGGEEEEEESS
T ss_pred             HHHHHHHHHhcCCcEEEEEeCCCEEEEEEEEECCcE-EEEECC------------ceEEEEeeeEEEEeEcc
Confidence            356888887  7899999999999999999999998 444421            24577777788877654

>1u1s_A HFQ protein; SM-like bacterial protein, riken structural genomics/proteomics initiative, RSGI, structural genomics, RNA binding protein; 1.60A {Pseudomonas aeruginosa} SCOP: b.38.1.2 PDB: 1u1t_A 3qui_A* 3m4g_A 3inz_A

Probab=97.27  E-value=0.00054  Score=41.49  Aligned_cols=37  Identities=30%  Similarity=0.382  Sum_probs=31.7

Q ss_pred             HHHHhhcC--CCEEEEEEcCccEEEEEEEEecCCcceEEc
Q psy6372          10 KPFLNLLT--GKSVICKLKWGHEYKGILVSTDGYMNCQLA   47 (88)
Q Consensus        10 ~~~L~~~i--~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~   47 (88)
                      -.||+.+.  +.+|+|-|.||..++|.+.+||+|+ +.|+
T Consensus         9 d~fLn~lrk~~~~Vtv~L~NG~~l~G~I~~fD~ft-VlL~   47 (82)
T 1u1s_A            9 DPYLNTLRKERVPVSIYLVNGIKLQGQIESFDQFV-ILLK   47 (82)
T ss_dssp             HHHHHHHHHTTCCEEEEETTSCEEEEEEEEECSSE-EEEE
T ss_pred             HHHHHHHHHcCCcEEEEEeCCcEEEEEEEEEcceE-EEEe
Confidence            46788775  7889999999999999999999999 4444

>3sb2_A Protein HFQ; SM-like, RNA chaperone, chaperone; 2.63A {Herbaspirillum seropedicae} SCOP: b.38.1.2

Probab=97.27  E-value=0.00056  Score=41.13  Aligned_cols=65  Identities=26%  Similarity=0.234  Sum_probs=44.1

Q ss_pred             CCCCCCCCcHHHHhhcC--CCEEEEEEcCccEEEEEEEEecCCcceEEcceEEEecCeeeeeeceEEEeCCcEEEEEcCC
Q psy6372           1 MSTPLPCNPKPFLNLLT--GKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTGKLGEVLIRCNNILYIRGAE   78 (88)
Q Consensus         1 m~~~~~~~p~~~L~~~i--~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~d~~e~~~~~~~~~~~~v~IrG~~I~~I~~~d   78 (88)
                      |+++....--.||..+.  ..+|+|.|.||..++|++.+||+|+ +.|+      +++      ..+|.=..|.+|.+..
T Consensus         1 m~~~~~nlQd~fLn~lrk~k~~VtI~LvnG~~L~G~I~~fD~f~-VlL~------~g~------~qLIYKhAISTI~P~~   67 (79)
T 3sb2_A            1 MSNKGQLLQDPFLNALRKEHVPVSIYLVNGIKLQGHVESFDQYV-VLLR------NTV------TQMVYKHAISTVVPAR   67 (79)
T ss_dssp             -----CTTHHHHHHHHHHTTCCEEEEETTSCEEEEEEEEECSSE-EEEE------SSS------EEEEEGGGEEEEEESS
T ss_pred             CCccccchHHHHHHHHHhcCCeEEEEEeCCCEEEEEEEEECCcE-EEEE------CCc------eEEEEeeeEEEEeecC
Confidence            55554444467888885  5669999999999999999999998 4443      232      3466677777776543

>3ahu_A Protein HFQ; SM-like motif, protein-RNA complex, translation-RNA complex; 2.20A {Bacillus subtilis} PDB: 3hsb_A

Probab=97.18  E-value=0.00054  Score=41.12  Aligned_cols=36  Identities=22%  Similarity=0.286  Sum_probs=31.5

Q ss_pred             HHHHhhcC--CCEEEEEEcCccEEEEEEEEecCCcceE
Q psy6372          10 KPFLNLLT--GKSVICKLKWGHEYKGILVSTDGYMNCQ   45 (88)
Q Consensus        10 ~~~L~~~i--~k~V~V~L~~g~~~~G~L~~~D~~mNlv   45 (88)
                      -.||+.+.  +.+|+|-|.||..++|.+.+||+|+=+.
T Consensus        13 d~fLn~lrk~~~~Vtv~L~nG~~l~G~I~~fD~f~VlL   50 (78)
T 3ahu_A           13 DQFLNQIRKENTYVTVFLLNGFQLRGQVKGFDNFTVLL   50 (78)
T ss_dssp             HHHHHHHHHHTCCEEEEETTSCEEEEEEEEECSSEEEE
T ss_pred             HHHHHHHHHcCCcEEEEEeCCeEEEEEEEEEcceEEEE
Confidence            46888886  8899999999999999999999998443

>2y90_A Protein HFQ; RNA-binding protein, SM-like, RNA chaperone; 2.25A {Escherichia coli} PDB: 3qhs_A

Probab=97.09  E-value=0.00065  Score=42.78  Aligned_cols=38  Identities=32%  Similarity=0.388  Sum_probs=31.7

Q ss_pred             cHHHHhhcCC--CEEEEEEcCccEEEEEEEEecCCcceEEc
Q psy6372           9 PKPFLNLLTG--KSVICKLKWGHEYKGILVSTDGYMNCQLA   47 (88)
Q Consensus         9 p~~~L~~~i~--k~V~V~L~~g~~~~G~L~~~D~~mNlvL~   47 (88)
                      =-.||+.+..  .+|+|.|.||..++|++.+||+|+ +.|+
T Consensus        10 Qd~fLn~lrk~k~~VtI~LvNG~~L~G~I~~fD~f~-VlL~   49 (104)
T 2y90_A           10 QDPFLNALRRERVPVSIYLVNGIKLQGQIESFDQFV-ILLK   49 (104)
T ss_dssp             HHHHHHHHHHTTCCEEEEETTSCEEEEEEEEECSSE-EEEE
T ss_pred             HHHHHHHHHhcCCcEEEEEeCCCEEEEEEEEECCcE-EEEE
Confidence            3468888864  489999999999999999999998 4444

>3hfo_A SSR3341 protein; HFQ, SM, RNA-binding protein, sRNA, translational regulation binding protein; 1.30A {Synechocystis SP}

Probab=97.08  E-value=0.0021  Score=37.79  Aligned_cols=65  Identities=25%  Similarity=0.174  Sum_probs=45.9

Q ss_pred             CCCCCCCCc-HHHHhhcC--CCEEEEEEcCccEEEEEEEEecCCcceEEcceEEEecCeeeeeeceEEEeCCcEEEEEc
Q psy6372           1 MSTPLPCNP-KPFLNLLT--GKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTGKLGEVLIRCNNILYIRG   76 (88)
Q Consensus         1 m~~~~~~~p-~~~L~~~i--~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~d~~e~~~~~~~~~~~~v~IrG~~I~~I~~   76 (88)
                      |+.--+..| ...|+.++  ..+|.|+|.+|..+.|++..+|+++ +.|.+..    +      ...+|.-..|.||.+
T Consensus         1 m~~fdt~lPsvR~lQ~~ik~k~~V~I~L~tG~~l~G~i~WQD~~c-l~L~~~~----~------~~~LI~r~AI~~I~p   68 (70)
T 3hfo_A            1 MSRFDSGLPSVRQVQLLIKDQTPVEIKLLTGDSLFGTIRWQDTDG-LGLVDDS----E------RSTIVRLAAIAYITP   68 (70)
T ss_dssp             ----CCSCHHHHHHHHHHHHTCEEEEEETTSCEEEEEEEEECSSE-EEEECTT----C------CEEEEEGGGEEEEEE
T ss_pred             CCcccCCCCcHHHHHHHHhhCceEEEEecCCCEEEEEEEEeCCCE-EEEEcCC----C------CeEEEEeeeeEEEee
Confidence            666667777 46788886  6889999999999999999999998 4443321    1      234677777777764

>3hfn_A ASL2047 protein; HFQ, SM, RNA-binding protein, sRNA, translational regulation binding protein; 2.31A {Nostoc SP}

Probab=96.98  E-value=0.0035  Score=36.98  Aligned_cols=65  Identities=20%  Similarity=0.159  Sum_probs=44.1

Q ss_pred             CCCCCCCCc-HHHHhhcC--CCEEEEEEcCccEEEEEEEEecCCcceEEcceEEEecCeeeeeeceEEEeCCcEEEEEc
Q psy6372           1 MSTPLPCNP-KPFLNLLT--GKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTGKLGEVLIRCNNILYIRG   76 (88)
Q Consensus         1 m~~~~~~~p-~~~L~~~i--~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~d~~e~~~~~~~~~~~~v~IrG~~I~~I~~   76 (88)
                      ||.--+..| ...|+.++  .++|.|+|.+|..+.|++.-+|+++ +.|.+...          ..++|.-..|.||.+
T Consensus         3 ~~~fdt~lPsvR~lQ~~Ik~k~~V~I~L~tGd~l~G~i~WQD~~c-l~L~~~~~----------~~~LI~R~AI~~Ikp   70 (72)
T 3hfn_A            3 ITEFDTSLPSIRQLQNLIKQAAPVEIKLVTGDAITGRVLWQDPTC-VCIADENS----------RQTTIWKQAIAYLQP   70 (72)
T ss_dssp             ------CHHHHHHHHHHHSSCCEEEEEETTSCEEEEEEEEECSSE-EEEEC-------------CEEEEEGGGEEEEEE
T ss_pred             ccccCCCCCcHHHHHHHHhhCceEEEEecCCCEEEEEEEEECCCE-EEEEcCCC----------CeEEEEeeeeEEEEe
Confidence            444445556 46788886  5779999999999999999999998 44443321          246777888888865

>1kq1_A HFQ, HOST factor for Q beta; hexamer, RNA binding protein, translational regulator, SM motif; 1.55A {Staphylococcus aureus} SCOP: b.38.1.2 PDB: 1kq2_A

Probab=96.96  E-value=0.0055  Score=36.53  Aligned_cols=36  Identities=19%  Similarity=0.243  Sum_probs=31.5

Q ss_pred             HHHHhhcC--CCEEEEEEcCccEEEEEEEEecCCcceE
Q psy6372          10 KPFLNLLT--GKSVICKLKWGHEYKGILVSTDGYMNCQ   45 (88)
Q Consensus        10 ~~~L~~~i--~k~V~V~L~~g~~~~G~L~~~D~~mNlv   45 (88)
                      -.||+.+.  +.+|+|.|.||-.++|++.+||+|+=+.
T Consensus         9 d~fLn~lrk~k~~VtI~L~nG~~l~G~I~~fD~f~VlL   46 (77)
T 1kq1_A            9 DKALENFKANQTEVTVFFLNGFQMKGVIEEYDKYVVSL   46 (77)
T ss_dssp             HHHHHHHHHHTCEEEEEETTSCEEEEEEEEECSSEEEE
T ss_pred             HHHHHHHHhcCCeEEEEEeCCCEEEEEEEEECCcEEEE
Confidence            35888887  8899999999999999999999998443

>4a53_A EDC3; RNA binding protein; NMR {Schizosaccharomyces pombe} PDB: 4a54_A

Probab=96.88  E-value=0.0027  Score=41.08  Aligned_cols=57  Identities=18%  Similarity=0.170  Sum_probs=43.0

Q ss_pred             HhhcCCCEEEEEEcCccEEEEEEEEecCCcceEE--cceEEEecCeeeeeeceEEEeCCcEEEEEcCCCC
Q psy6372          13 LNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQL--ASTEEIIDGHCTGKLGEVLIRCNNILYIRGAEEG   80 (88)
Q Consensus        13 L~~~i~k~V~V~L~~g~~~~G~L~~~D~~mNlvL--~d~~e~~~~~~~~~~~~v~IrG~~I~~I~~~d~~   80 (88)
                      +..++|..|.|+|++|..++|++..+|.. +|+|  ++|....          .-|+...|.-+.+.+-.
T Consensus         7 ~sqFlGy~V~v~LkDgs~~qG~I~~vd~k-~LtL~~~~a~~s~----------~~I~asdI~DLkVl~~~   65 (125)
T 4a53_A            7 VADFYGSNVEVLLNNDSKARGVITNFDSS-NSILQLRLANDST----------KSIVTKDIKDLRILPKN   65 (125)
T ss_dssp             HHHHTTCEEEEEETTSCEEEEEEEEEETT-TTEEEEEETTTEE----------EEEEGGGEEEEEECCSC
T ss_pred             HHHhcCceEEEEECCCCEeeEEEEeecCC-eeEEecccccccc----------ceeecccccceeeeecc
Confidence            46789999999999999999999999844 4666  8885321          16777777766655443

>2fb7_A SM-like protein, LSM-14_N (RAP55); DR.13312, BC055387, AAH55387, stronGly BENT five-stranded antiparallel beta- sheet, structural genomics, PSI; NMR {Danio rerio} SCOP: b.38.1.5 PDB: 2vxf_A

Probab=96.79  E-value=0.0037  Score=38.68  Aligned_cols=70  Identities=17%  Similarity=0.151  Sum_probs=52.6

Q ss_pred             cHHHHhhcCCCEEEEEEcCccEEEEEEEEec-CCcceEEcceEEE-ecC--------eeeeeeceEEEeCCcEEEEEcCC
Q psy6372           9 PKPFLNLLTGKSVICKLKWGHEYKGILVSTD-GYMNCQLASTEEI-IDG--------HCTGKLGEVLIRCNNILYIRGAE   78 (88)
Q Consensus         9 p~~~L~~~i~k~V~V~L~~g~~~~G~L~~~D-~~mNlvL~d~~e~-~~~--------~~~~~~~~v~IrG~~I~~I~~~d   78 (88)
                      |..--..++|++|.+..+.+-.|.|+|..+| +..-+.|.|+..+ .+|        ....-++.+..||+.|.-+.+-+
T Consensus        10 ~~~~~~~~IGs~ISLISk~dIRYeGiL~~In~~~sTiaL~nVRsfGTEgR~~~~~ipp~~~vyeyIvFrGsDIKDL~V~e   89 (95)
T 2fb7_A           10 DPSGGTPYIGSKISLISKAEIRYEGILYTIDTENSTVALAKVRSFGTEDRPTDRPIAPRDETFEYIIFRGSDIKDLTVCE   89 (95)
T ss_dssp             ------CCSSEEEEEEETTTEEEEEEEEEEETTTTEEEEESCCCCSCCSSSCSSCCCSCCCCSSCEEECSTTEEEEEESC
T ss_pred             CCCccCcccCCeEEEEECCCceEEEEEecccCccCEEEEEeeeEecccCCCCCCccCCCCcceeEEEEcCCCcceEEEec
Confidence            3444567899999999999999999999999 5678999998864 221        13446789999999999887643

>2vc8_A Enhancer of mRNA-decapping protein 3; P-BODY component, cytoplasm, SM-like protein, protein-binding; 1.31A {Homo sapiens}

Probab=96.70  E-value=0.0081  Score=36.38  Aligned_cols=63  Identities=19%  Similarity=0.122  Sum_probs=51.5

Q ss_pred             hhcCCCEEEEEEcCcc-EEEEEEEEecCC-cceEEcceEEEecCeeeeeeceEEEeCCcEEEEEcCCC
Q psy6372          14 NLLTGKSVICKLKWGH-EYKGILVSTDGY-MNCQLASTEEIIDGHCTGKLGEVLIRCNNILYIRGAEE   79 (88)
Q Consensus        14 ~~~i~k~V~V~L~~g~-~~~G~L~~~D~~-mNlvL~d~~e~~~~~~~~~~~~v~IrG~~I~~I~~~d~   79 (88)
                      .+++|+.|.++-+++- .|+|.|..+|.. -||.|.++.  .+|- +.....|.+++.-|.-+.+.+-
T Consensus         5 ~~~iGs~VSi~c~d~lGvYQG~i~~vd~~~~tItL~~~f--~NG~-~~~s~eVtls~~DI~~L~ii~~   69 (84)
T 2vc8_A            5 TDWLGSIVSINCGDSLGVYQGRVSAVDQVSQTISLTRPF--HNGV-KCLVPEVTFRAGDITELKILEI   69 (84)
T ss_dssp             CTTTTCEEEEECCTTTCEEEEEEEEEETTTTEEEEEEEE--ETTE-ECSSSEEEEEGGGCSEEEEEEC
T ss_pred             ccccCCEEEEEECCCceEEEEEEEEeccCCCeEEEehhh--hCCC-CCCCcEEEEEecChhheEEEec
Confidence            4689999999999998 999999999965 789999994  4664 4555779999998877765443

>2qtx_A Uncharacterized protein MJ1435; HFQ, SM, RNA-binding protein, sRNA, translational regulation, RNA binding protein; 2.50A {Methanocaldococcus jannaschii}

Probab=96.34  E-value=0.009  Score=35.12  Aligned_cols=34  Identities=21%  Similarity=0.168  Sum_probs=28.0

Q ss_pred             HHhhc--CCCEEEEEEcCccEEEEEEEEecCCcceE
Q psy6372          12 FLNLL--TGKSVICKLKWGHEYKGILVSTDGYMNCQ   45 (88)
Q Consensus        12 ~L~~~--i~k~V~V~L~~g~~~~G~L~~~D~~mNlv   45 (88)
                      ||+.+  -+.+|+|-|.||..++|.+.+||+|+=+.
T Consensus        17 fLn~~r~~~~~Vtv~L~NG~~l~G~I~~fD~ftVll   52 (71)
T 2qtx_A           17 FEYARRLNGKKVKIFLRNGEVLDAEVTGVSNYEIMV   52 (71)
T ss_dssp             CCGGGGGTTCEEEEEETTSCEEEEEEEEECSSEEEE
T ss_pred             HHHHHHHcCCcEEEEEeCCeEEEEEEEEEcceEEEE
Confidence            44444  46789999999999999999999998443

>1y96_B Gemin7, SIP3, GEM-associated protein 7; SM fold, protein complex, RNA binding protein; 2.00A {Homo sapiens}

Probab=96.26  E-value=0.023  Score=34.41  Aligned_cols=63  Identities=22%  Similarity=0.226  Sum_probs=49.3

Q ss_pred             HHHHhhcCCCEEEEEEcCccEEEEEEEEec-CCcceEEcceEEEecCeeeeeeceEEEeCCcEEEEEcC
Q psy6372          10 KPFLNLLTGKSVICKLKWGHEYKGILVSTD-GYMNCQLASTEEIIDGHCTGKLGEVLIRCNNILYIRGA   77 (88)
Q Consensus        10 ~~~L~~~i~k~V~V~L~~g~~~~G~L~~~D-~~mNlvL~d~~e~~~~~~~~~~~~v~IrG~~I~~I~~~   77 (88)
                      +.+|..+.|++|.+.+.++.+..|++.++| ...|+..++-+ +.=|    .++.-.+|+.-|.++...
T Consensus        21 Lr~l~~m~~~~v~f~m~E~t~V~a~F~a~d~d~~~f~Vs~L~-TPiG----v~~eAlLR~~Dii~~sF~   84 (85)
T 1y96_B           21 LRSLLAMVGHQVSFTLHEGVRVAAHFGATDLDVANFYVSQLQ-TPIG----VQAEALLRCSDIISYTFK   84 (85)
T ss_dssp             HHHHHHHTTSEEEEEEGGGCEEEEEEEEECTTCCEEEEEEEC-CTTC----CEEEEEEEGGGEEEEEEC
T ss_pred             HHHHHHhCCCceEEEEeCCeEEEEEEEecCcccceeEhhhcC-CCcc----cchhhhhhcCCEEEEEec
Confidence            457788899999999999999999999999 55777655544 2112    356789999999988753

>1ycy_A Conserved hypothetical protein; structural genomics, southeast collaboratory for structural genomics, secsg, protein structure initiative; 2.80A {Pyrococcus furiosus} SCOP: b.38.1.4

Probab=96.24  E-value=0.035  Score=32.12  Aligned_cols=61  Identities=23%  Similarity=0.316  Sum_probs=43.1

Q ss_pred             HHHhhcCCCEEEEEEcCccEEEEEEEEecCCcceEEcceEEEecCeeeeeeceEEEeCCcEEEEEc
Q psy6372          11 PFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTGKLGEVLIRCNNILYIRG   76 (88)
Q Consensus        11 ~~L~~~i~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~d~~e~~~~~~~~~~~~v~IrG~~I~~I~~   76 (88)
                      ..|....|++|-+.......++|+|..||.-. +.|+|++... |+   +-..++++=+.|-.|.+
T Consensus         9 ktL~~WKg~rvAv~vg~ehSFtGiledFDeEv-iLL~dV~D~~-GN---k~k~liv~idDinWimL   69 (71)
T 1ycy_A            9 KVLKEWKGHKVAVSVGGDHSFTGTLEDFDEEV-ILLKDVVDVI-GN---RGKQMLIGLEDINWIML   69 (71)
T ss_dssp             HHHHHHTTSEEEEEEC----CEEEEEEECSSE-EEEEEEEETT-EE---EEEEEEEEGGGEEEEEE
T ss_pred             HHHHHhCCcEEEEEecCcceeeeehhhcCcce-eehhhHHHHh-cc---ccceeEEEeccceEEEe
Confidence            57888899999999999999999999999987 7889999762 22   22355666666655544

>1ib8_A Conserved protein SP14.3; nucleic acid binding protein, ribosomal protein, essential gene, structural genomics; NMR {Streptococcus pneumoniae} SCOP: b.38.2.1 d.52.4.1

Probab=93.41  E-value=0.06  Score=35.77  Aligned_cols=44  Identities=16%  Similarity=0.165  Sum_probs=33.6

Q ss_pred             CCCCCCCcHH---HHhhcCCCEEEEEE----cCccEEEEEEEEecCCcceEE
Q psy6372           2 STPLPCNPKP---FLNLLTGKSVICKL----KWGHEYKGILVSTDGYMNCQL   46 (88)
Q Consensus         2 ~~~~~~~p~~---~L~~~i~k~V~V~L----~~g~~~~G~L~~~D~~mNlvL   46 (88)
                      ||+...-|+.   -+..++|+.|.|+|    .+.+.++|+|.++|+.. ++|
T Consensus        85 SSPGldRpL~~~~df~r~~G~~V~V~l~~~~~g~k~~~G~L~~~~~~~-v~l  135 (164)
T 1ib8_A           85 TSPGLERPLKTKDAVAGAVGKYIHVGLYQAIDKQKVFEGTLLAFEEDE-LTM  135 (164)
T ss_dssp             ECCSSSSCCSSHHHHHHHCSEEEEEECSSCSSSCSEEEEEEEEEETTE-EEE
T ss_pred             eCCCCCCCCCCHHHHHHhCCcEEEEEEecccCCceEEEEEEEEEeCCE-EEE
Confidence            6676677764   45577999999999    34599999999999753 444

>3rux_A BIRA bifunctional protein; biotin-protein ligase, ligase-ligase inhibitor complex; HET: BS5; 1.70A {Mycobacterium tuberculosis} PDB: 3l1a_A 3l2z_A 2cgh_A

Probab=92.30  E-value=0.29  Score=34.62  Aligned_cols=34  Identities=24%  Similarity=0.186  Sum_probs=30.4

Q ss_pred             cCCCEEEEEEcCccEEEEEEEEecCCcceEEcce
Q psy6372          16 LTGKSVICKLKWGHEYKGILVSTDGYMNCQLAST   49 (88)
Q Consensus        16 ~i~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~d~   49 (88)
                      .+|++|++.+.+|..+.|+..++|+...|+++..
T Consensus       222 ~~g~~V~v~~~~~~~~~G~~~gId~~G~L~v~~~  255 (270)
T 3rux_A          222 TIGSRVRVELPGGQDVVGIARDIDDQGRLCLDVG  255 (270)
T ss_dssp             STTSEEEEECTTSCEEEEEEEEECTTSCEEEEET
T ss_pred             ccCCEEEEEECCCeEEEEEEEEECCCCeEEEEEC
Confidence            3699999999889999999999999999998654

>1sg5_A ORF, hypothetical protein; A+B protein, montreal-kingston bacterial structural genomics initiative, BSGI, structural genomics, transcription; NMR {Escherichia coli} SCOP: b.137.1.2

Probab=89.56  E-value=0.21  Score=30.03  Aligned_cols=38  Identities=18%  Similarity=0.050  Sum_probs=30.3

Q ss_pred             CCCCCCCCcHH-------HHhhcCCCEEEEEEcCccEEEEEEEEe
Q psy6372           1 MSTPLPCNPKP-------FLNLLTGKSVICKLKWGHEYKGILVST   38 (88)
Q Consensus         1 m~~~~~~~p~~-------~L~~~i~k~V~V~L~~g~~~~G~L~~~   38 (88)
                      ||...+..|..       .+....+.+++|+|+||..+.|+....
T Consensus         1 m~~~~~Y~pI~Cd~yD~LElAc~~~~~l~l~l~dGe~~~g~a~D~   45 (86)
T 1sg5_A            1 MSMNDTYQPINCDDYDNLELACQHHLMLTLELKDGEKLQAKASDL   45 (86)
T ss_dssp             CCCCCCCCSSCCSSHHHHHHHHTTTTCEEEECTTTCCEEESSCEE
T ss_pred             CCCCCCceeechhhhhHHHHHHHcCCeEEEEEeCCCEEEEEEEee
Confidence            77778888863       556678999999999999999965543

>1bia_A BIRA bifunctional protein; transcription regulation; 2.30A {Escherichia coli} SCOP: a.4.5.1 b.34.1.1 d.104.1.2 PDB: 1bib_A* 1hxd_A* 2ewn_A*

Probab=89.45  E-value=0.89  Score=32.56  Aligned_cols=48  Identities=19%  Similarity=0.040  Sum_probs=34.7

Q ss_pred             cCCCEEEEEEcCccEEEEEEEEecCCcceEEcceEEEecCeeeeeeceEEEeC
Q psy6372          16 LTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTGKLGEVLIRC   68 (88)
Q Consensus        16 ~i~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~d~~e~~~~~~~~~~~~v~IrG   68 (88)
                      ..|++|++...+ ..+.|+..++|+...|+++....    ......|.|.+|+
T Consensus       271 ~~g~~V~v~~~~-~~~~G~~~gid~~G~L~v~~~~g----~~~~~~Gev~~r~  318 (321)
T 1bia_A          271 FINRPVKLIIGD-KEIFGISRGIDKQGALLLEQDGI----IKPWMGGEISLRS  318 (321)
T ss_dssp             TTTSEEEEEETT-EEEEEEEEEECTTSCEEEEETTE----EEEESSCEEEEC-
T ss_pred             hcCCEEEEEECC-cEEEEEEEEECCCCeEEEEECCC----EEEEEeeeEEEec
Confidence            379999998764 57999999999999999864321    1234446676664

>2eay_A Biotin [acetyl-COA-carboxylase] ligase; biotin biosynthesis, dimer, X-RAY diffraction, structural genomics, NPPSFA; 1.95A {Aquifex aeolicus} PDB: 3efs_A* 3fjp_A 3efr_A*

Probab=89.41  E-value=0.32  Score=33.53  Aligned_cols=47  Identities=19%  Similarity=0.041  Sum_probs=33.8

Q ss_pred             cCCCEEEEEEcCccEEEEEEEEecCCcceEEcceEEEecCeeeeeeceEEEeC
Q psy6372          16 LTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTGKLGEVLIRC   68 (88)
Q Consensus        16 ~i~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~d~~e~~~~~~~~~~~~v~IrG   68 (88)
                      .+|++|++...++  +.|+..++|+...|+++....    ......|.|.+|+
T Consensus       186 ~~g~~V~v~~~~~--~~G~~~gId~~G~L~v~~~~G----~~~~~~Gev~~r~  232 (233)
T 2eay_A          186 YLGEEVKLLGEGK--ITGKLVGLSEKGGALILTEEG----IKEILSGEFSLRR  232 (233)
T ss_dssp             TTTSEEEETTEEE--EEEEEEEECTTSCEEEEETTE----EEEECSCCEEEC-
T ss_pred             ccCCEEEEEECCe--EEEEEEEECCCCeEEEEECCC----eEEEEEeEEEEec
Confidence            3799999987655  999999999999999864321    1233446677664

>2ej9_A Putative biotin ligase; biotin biosynthesis, monomer, X-RAY diffraction, structural genomics, NPPSFA; HET: BTN; 2.00A {Methanocaldococcus jannaschii}

Probab=88.36  E-value=1.4  Score=30.40  Aligned_cols=32  Identities=19%  Similarity=0.004  Sum_probs=28.4

Q ss_pred             cCCCEEEEEEcCccEEEEEEEEecCCcceEEcc
Q psy6372          16 LTGKSVICKLKWGHEYKGILVSTDGYMNCQLAS   48 (88)
Q Consensus        16 ~i~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~d   48 (88)
                      .+|++|++...++..+.|+..++|+...|+ +.
T Consensus       190 ~~g~~V~v~~~~~~~~~G~~~gId~~G~L~-~~  221 (237)
T 2ej9_A          190 TIGKQVKILLSNNEIITGKVYDIDFDGIVL-GT  221 (237)
T ss_dssp             STTCEEEEEETTSCEEEEEEEEECSSEEEE-EE
T ss_pred             ccCCEEEEEECCCeEEEEEEEEECCCCeEE-Ec
Confidence            379999999988877999999999999998 53

>2xk0_A Polycomb protein PCL; transcription, aromatic CAGE; NMR {Drosophila melanogaster}

Probab=86.49  E-value=1.1  Score=25.99  Aligned_cols=39  Identities=21%  Similarity=0.321  Sum_probs=28.2

Q ss_pred             CCCCCCcHHHHhhcCCCEEEEEEcCccEEEEEEEEecCC
Q psy6372           3 TPLPCNPKPFLNLLTGKSVICKLKWGHEYKGILVSTDGY   41 (88)
Q Consensus         3 ~~~~~~p~~~L~~~i~k~V~V~L~~g~~~~G~L~~~D~~   41 (88)
                      +..|..|..-..--+|..|.++-.||+.|-|+++.....
T Consensus         4 ~pp~~a~~pa~~~~~geDVL~rw~DG~fYLGtIVd~~~~   42 (69)
T 2xk0_A            4 APPVAAPSPAVTYALQEDVFIKCNDGRFYLGTIIDQTSD   42 (69)
T ss_dssp             SCSSSSSCCCCCCCTTCEEEEECTTSCEEEEEEEEECSS
T ss_pred             CCCCCCCCcccccccCCeEEEEecCCCEEEEEEEecCCc
Confidence            344445544444457999999999999999999666543

>2rm4_A CG6311-PB, DM EDC3; enhancer of mRNA decapping, P-BODY component, SM-like protein,, protein binding; NMR {Drosophila melanogaster}

Probab=86.34  E-value=4.2  Score=25.09  Aligned_cols=62  Identities=16%  Similarity=0.200  Sum_probs=48.7

Q ss_pred             hhcCCCEEEEEEcCcc-EEEEEEEEecCCcceEEcceEEEecCe-eeeeeceEEEeCCcEEEEEcCC
Q psy6372          14 NLLTGKSVICKLKWGH-EYKGILVSTDGYMNCQLASTEEIIDGH-CTGKLGEVLIRCNNILYIRGAE   78 (88)
Q Consensus        14 ~~~i~k~V~V~L~~g~-~~~G~L~~~D~~mNlvL~d~~e~~~~~-~~~~~~~v~IrG~~I~~I~~~d   78 (88)
                      .+++|+.|.|.-.+.- .|+|.+..+|+ -+++|.++..  +|- -+.....|.++..-|..+.+.+
T Consensus         8 edwiG~~VSI~C~d~LGVyQG~I~~V~~-~~ItL~kaFr--NGiplk~~~~EVtLsa~DI~~L~IIe   71 (103)
T 2rm4_A            8 QDWIGCAVSIACDEVLGVFQGLIKQISA-EEITIVRAFR--NGVPLRKQNAEVVLKCTDIRSIDLIE   71 (103)
T ss_dssp             GGGTTCEEEEEECTTTCEEEEEEEEEET-TEEEEEEEEE--TTEECSCSSSCEEEETTTEEEEEEEE
T ss_pred             cceeceEEEEeeCCcceEeeEEEEEccc-ceeEEhhhhh--cCcCcCCCCceEEEEecchhheeeec
Confidence            3789999999999986 99999999996 4499998875  342 1345678899999888775543

>2e12_A SM-like motif, hypothetical protein XCC3642; novel SM-like motif, LSM motif, X- RAY crystallography, translation; 1.70A {Xanthomonas campestris PV}

Probab=81.01  E-value=1.9  Score=26.35  Aligned_cols=18  Identities=22%  Similarity=0.215  Sum_probs=16.5

Q ss_pred             CCEEEEEEcCccEEEEEE
Q psy6372          18 GKSVICKLKWGHEYKGIL   35 (88)
Q Consensus        18 ~k~V~V~L~~g~~~~G~L   35 (88)
                      ..+|+++|.+|+.+.||+
T Consensus        28 q~~v~i~l~DGs~l~GTv   45 (101)
T 2e12_A           28 QERVRIELDDGSMIAGTV   45 (101)
T ss_dssp             TCEEEEEETTSCEEEEEE
T ss_pred             eeEEEEEEcCCCeEeeee
Confidence            368999999999999997

---

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST

Original result of RPS-BLAST against SCOP70(version1.75) database

ID	Length	Definition	E-value
Query	88
d1i4k1_	72	b.38.1.1 (1:) Archaeal homoheptameric Sm protein {	9e-25
d1mgqa_	74	b.38.1.1 (A:) Archaeal homoheptameric Sm protein {	2e-23
d1h641_	71	b.38.1.1 (1:) Archaeal homoheptameric Sm protein {	3e-22
d1n9ra_	68	b.38.1.1 (A:) Small nuclear ribonucleoprotein F, S	5e-22
d1d3ba_	72	b.38.1.1 (A:) D3 core SNRNP protein {Human (Homo s	6e-22
d1b34a_	80	b.38.1.1 (A:) D1 core SNRNP protein {Human (Homo s	3e-21
d1i8fa_	71	b.38.1.1 (A:) Archaeal homoheptameric Sm protein {	9e-21
d1th7a1	76	b.38.1.1 (A:3-78) Archaeal homoheptameric Sm prote	1e-20
d1ljoa_	75	b.38.1.1 (A:) Archaeal homoheptameric Sm protein {	5e-20
d1m5q1_	127	b.38.1.1 (1:) Sm-Like archaeal protein Smap3 {Arch	7e-18
d2fwka1	92	b.38.1.1 (A:24-115) U6 snRNA-associated sm-like pr	5e-14
d1d3bb_	81	b.38.1.1 (B:) B core SNRNP protein {Human (Homo sa	5e-13
d1b34b_	93	b.38.1.1 (B:) D2 core SNRNP protein {Human (Homo s	5e-05

>d1i4k1_ b.38.1.1 (1:) Archaeal homoheptameric Sm protein {Archaeon Archaeoglobus fulgidus, AF-Sm1 [TaxId: 2234]} Length = 72

class: All beta proteins
fold: Sm-like fold
superfamily: Sm-like ribonucleoproteins
family: Sm motif of small nuclear ribonucleoproteins, SNRNP
domain: Archaeal homoheptameric Sm protein
species: Archaeon Archaeoglobus fulgidus, AF-Sm1 [TaxId: 2234]

 Score = 85.9 bits (213), Expect = 9e-25
 Identities = 26/72 (36%), Positives = 38/72 (52%)

Query: 6  PCNPKPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTGKLGEVL 65
          P  P   LN      VI +LK G E++G L   D +MN  L   EEI +G    K+G V+
Sbjct: 1  PPRPLDVLNRSLKSPVIVRLKGGREFRGTLDGYDIHMNLVLLDAEEIQNGEVVRKVGSVV 60

Query: 66 IRCNNILYIRGA 77
          IR + ++++  A
Sbjct: 61 IRGDTVVFVSPA 72

>d1mgqa_ b.38.1.1 (A:) Archaeal homoheptameric Sm protein {Archaeon Methanobacterium thermoautotrophicum [TaxId: 145262]} Length = 74

class: All beta proteins
fold: Sm-like fold
superfamily: Sm-like ribonucleoproteins
family: Sm motif of small nuclear ribonucleoproteins, SNRNP
domain: Archaeal homoheptameric Sm protein
species: Archaeon Methanobacterium thermoautotrophicum [TaxId: 145262]

 Score = 82.8 bits (205), Expect = 2e-23
 Identities = 30/67 (44%), Positives = 38/67 (56%)

Query: 8  NPKPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTGKLGEVLIR 67
           P   L       VI KLK   E++G+L S D +MN  L   EE+ DG  T +LG VLIR
Sbjct: 6  RPLDALGNSLNSPVIIKLKGDREFRGVLKSFDLHMNLVLNDAEELEDGEVTRRLGTVLIR 65

Query: 68 CNNILYI 74
           +NI+YI
Sbjct: 66 GDNIVYI 72

>d1h641_ b.38.1.1 (1:) Archaeal homoheptameric Sm protein {Archaeon Pyrococcus abyssi [TaxId: 29292]} Length = 71

class: All beta proteins
fold: Sm-like fold
superfamily: Sm-like ribonucleoproteins
family: Sm motif of small nuclear ribonucleoproteins, SNRNP
domain: Archaeal homoheptameric Sm protein
species: Archaeon Pyrococcus abyssi [TaxId: 29292]

 Score = 79.7 bits (197), Expect = 3e-22
 Identities = 23/67 (34%), Positives = 37/67 (55%)

Query: 8  NPKPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTGKLGEVLIR 67
           P   ++    K V+  LK G E++G L+  D ++N  LA  E I DG    + G+++IR
Sbjct: 2  RPLDVIHRSLDKDVLVILKKGFEFRGRLIGYDIHLNVVLADAEMIQDGEVVKRYGKIVIR 61

Query: 68 CNNILYI 74
           +N+L I
Sbjct: 62 GDNVLAI 68

>d1n9ra_ b.38.1.1 (A:) Small nuclear ribonucleoprotein F, Smf {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 68

class: All beta proteins
fold: Sm-like fold
superfamily: Sm-like ribonucleoproteins
family: Sm motif of small nuclear ribonucleoproteins, SNRNP
domain: Small nuclear ribonucleoprotein F, Smf
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 79.0 bits (195), Expect = 5e-22
 Identities = 34/68 (50%), Positives = 39/68 (57%), Gaps = 1/68 (1%)

Query: 13 LNLLTGKSVICKLKWGH-EYKGILVSTDGYMNCQLASTEEIIDGHCTGKLGEVLIRCNNI 71
          L  L    V  KLK+   EY+G LVSTD Y N QL   EE + G   G LGE+ IRCNN+
Sbjct: 1  LKGLVNHRVGVKLKFNSTEYRGTLVSTDNYFNLQLNEAEEFVAGVSHGTLGEIFIRCNNV 60

Query: 72 LYIRGAEE 79
          LYIR    
Sbjct: 61 LYIRELPN 68

>d1d3ba_ b.38.1.1 (A:) D3 core SNRNP protein {Human (Homo sapiens) [TaxId: 9606]} Length = 72

class: All beta proteins
fold: Sm-like fold
superfamily: Sm-like ribonucleoproteins
family: Sm motif of small nuclear ribonucleoproteins, SNRNP
domain: D3 core SNRNP protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 79.1 bits (195), Expect = 6e-22
 Identities = 18/67 (26%), Positives = 30/67 (44%)

Query: 9  PKPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTGKLGEVLIRC 68
          P   L+   G  V C+   G  Y+G L+  +  MNCQ+++           +L +V IR 
Sbjct: 3  PIKVLHEAEGHIVTCETNTGEVYRGKLIEAEDNMNCQMSNITVTYRDGRVAQLEQVYIRG 62

Query: 69 NNILYIR 75
            I ++ 
Sbjct: 63 CKIRFLI 69

>d1b34a_ b.38.1.1 (A:) D1 core SNRNP protein {Human (Homo sapiens) [TaxId: 9606]} Length = 80

class: All beta proteins
fold: Sm-like fold
superfamily: Sm-like ribonucleoproteins
family: Sm motif of small nuclear ribonucleoproteins, SNRNP
domain: D1 core SNRNP protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 77.4 bits (191), Expect = 3e-21
 Identities = 19/64 (29%), Positives = 30/64 (46%)

Query: 12 FLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTGKLGEVLIRCNNI 71
          FL  L+ ++V  +LK G +  G +   D  MN  L + +  +      +L  + IR NNI
Sbjct: 5  FLMKLSHETVTIELKNGTQVHGTITGVDVSMNTHLKAVKMTLKNREPVQLETLSIRGNNI 64

Query: 72 LYIR 75
           Y  
Sbjct: 65 RYFI 68

>d1i8fa_ b.38.1.1 (A:) Archaeal homoheptameric Sm protein {Archaeon Pyrobaculum aerophilum [TaxId: 13773]} Length = 71

class: All beta proteins
fold: Sm-like fold
superfamily: Sm-like ribonucleoproteins
family: Sm motif of small nuclear ribonucleoproteins, SNRNP
domain: Archaeal homoheptameric Sm protein
species: Archaeon Pyrobaculum aerophilum [TaxId: 13773]

 Score = 75.9 bits (187), Expect = 9e-21
 Identities = 27/64 (42%), Positives = 38/64 (59%), Gaps = 1/64 (1%)

Query: 12 FLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTGKLGEVLIRCNNI 71
           L    GK V+ KL+  HE +GIL S D ++N  L   EEIIDG+   K G +++R  N+
Sbjct: 6  TLQDSIGKQVLVKLRDSHEIRGILRSFDQHVNLLLEDAEEIIDGNVY-KRGTMVVRGENV 64

Query: 72 LYIR 75
          L+I 
Sbjct: 65 LFIS 68

>d1th7a1 b.38.1.1 (A:3-78) Archaeal homoheptameric Sm protein {Sulfolobus solfataricus [TaxId: 2287]} Length = 76

class: All beta proteins
fold: Sm-like fold
superfamily: Sm-like ribonucleoproteins
family: Sm motif of small nuclear ribonucleoproteins, SNRNP
domain: Archaeal homoheptameric Sm protein
species: Sulfolobus solfataricus [TaxId: 2287]

 Score = 75.5 bits (186), Expect = 1e-20
 Identities = 23/67 (34%), Positives = 34/67 (50%)

Query: 8  NPKPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTGKLGEVLIR 67
               L       V+ KLK   E +G+L S D +MN  L+ +EEI       KLG ++IR
Sbjct: 7  TAHKVLAESLNNLVLVKLKGNKEVRGMLRSYDQHMNLVLSDSEEIQSDGSGKKLGTIVIR 66

Query: 68 CNNILYI 74
           +N++ I
Sbjct: 67 GDNVILI 73

>d1ljoa_ b.38.1.1 (A:) Archaeal homoheptameric Sm protein {Archaeon Archaeoglobus fulgidus, AF-Sm2 [TaxId: 2234]} Length = 75

class: All beta proteins
fold: Sm-like fold
superfamily: Sm-like ribonucleoproteins
family: Sm motif of small nuclear ribonucleoproteins, SNRNP
domain: Archaeal homoheptameric Sm protein
species: Archaeon Archaeoglobus fulgidus, AF-Sm2 [TaxId: 2234]

 Score = 74.0 bits (182), Expect = 5e-20
 Identities = 19/69 (27%), Positives = 33/69 (47%), Gaps = 1/69 (1%)

Query: 8  NPKPFLNLLTGKSVICKLKWG-HEYKGILVSTDGYMNCQLASTEEIIDGHCTGKLGEVLI 66
           P   +  + GK +  ++K   ++  G L   D YMN  L +  E         LGE+++
Sbjct: 5  LPNQMVKSMVGKIIRVEMKGEENQLVGKLEGVDDYMNLYLTNAMECKGEEKVRSLGEIVL 64

Query: 67 RCNNILYIR 75
          R NN++ I+
Sbjct: 65 RGNNVVLIQ 73

>d1m5q1_ b.38.1.1 (1:) Sm-Like archaeal protein Smap3 {Archaeon Pyrobaculum aerophilum [TaxId: 13773]} Length = 127

class: All beta proteins
fold: Sm-like fold
superfamily: Sm-like ribonucleoproteins
family: Sm motif of small nuclear ribonucleoproteins, SNRNP
domain: Sm-Like archaeal protein Smap3
species: Archaeon Pyrobaculum aerophilum [TaxId: 13773]

 Score = 70.1 bits (172), Expect = 7e-18
 Identities = 21/68 (30%), Positives = 28/68 (41%), Gaps = 4/68 (5%)

Query: 12 FLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTGKLGEVLIRCNNI 71
           LN L G+ V   L  G  YKG+L + D  +N  LA+           K   V I    I
Sbjct: 4  ELNNLLGREVQVVLSNGEVYKGVLHAVDNQLNIVLANASNKAG----EKFNRVFIMYRYI 59

Query: 72 LYIRGAEE 79
          ++I   E 
Sbjct: 60 VHIDSTER 67

>d2fwka1 b.38.1.1 (A:24-115) U6 snRNA-associated sm-like protein LSM5 {Cryptosporidium parvum [TaxId: 5807]} Length = 92

class: All beta proteins
fold: Sm-like fold
superfamily: Sm-like ribonucleoproteins
family: Sm motif of small nuclear ribonucleoproteins, SNRNP
domain: U6 snRNA-associated sm-like protein LSM5
species: Cryptosporidium parvum [TaxId: 5807]

 Score = 59.5 bits (144), Expect = 5e-14
 Identities = 15/82 (18%), Positives = 28/82 (34%), Gaps = 15/82 (18%)

Query: 8  NPKPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEII-------------- 53
           P   ++   G  +   +K   E+ G+L   D Y+N  L   +E                
Sbjct: 5  LPLALIDKCIGNRIYVVMKGDKEFSGVLRGFDEYVNMVLDDVQEYGFKADEEDISGGNKK 64

Query: 54 -DGHCTGKLGEVLIRCNNILYI 74
                 +L  +L+  NN+  +
Sbjct: 65 LKRVMVNRLETILLSGNNVAML 86

>d1d3bb_ b.38.1.1 (B:) B core SNRNP protein {Human (Homo sapiens) [TaxId: 9606]} Length = 81

class: All beta proteins
fold: Sm-like fold
superfamily: Sm-like ribonucleoproteins
family: Sm motif of small nuclear ribonucleoproteins, SNRNP
domain: B core SNRNP protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 56.4 bits (136), Expect = 5e-13
 Identities = 15/67 (22%), Positives = 26/67 (38%), Gaps = 10/67 (14%)

Query: 18 GKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEII----------DGHCTGKLGEVLIR 67
             + C L+ G  + G   + D +MN  L   +E            +      LG VL+R
Sbjct: 8  DYRMRCILQDGRIFIGTFKAFDKHMNLILCDCDEFRKIKPKNSKQAEREEKRVLGLVLLR 67

Query: 68 CNNILYI 74
            N++ +
Sbjct: 68 GENLVSM 74

>d1b34b_ b.38.1.1 (B:) D2 core SNRNP protein {Human (Homo sapiens) [TaxId: 9606]} Length = 93

class: All beta proteins
fold: Sm-like fold
superfamily: Sm-like ribonucleoproteins
family: Sm motif of small nuclear ribonucleoproteins, SNRNP
domain: D2 core SNRNP protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 36.4 bits (84), Expect = 5e-05
 Identities = 7/77 (9%), Positives = 28/77 (36%), Gaps = 14/77 (18%)

Query: 12 FLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEII--------------DGHC 57
            ++     V+   +   +  G + + D + N  L + +E+                 + 
Sbjct: 8  TQSVKNNTQVLINCRNNKKLLGRVKAFDRHCNMVLENVKEMWTEVPKSGKGKKKSKPVNK 67

Query: 58 TGKLGEVLIRCNNILYI 74
             + ++ +R ++++ +
Sbjct: 68 DRYISKMFLRGDSVIVV 84

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	88
d1d3ba_	72	D3 core SNRNP protein {Human (Homo sapiens) [TaxId	99.94
d1i4k1_	72	Archaeal homoheptameric Sm protein {Archaeon Archa	99.94
d1h641_	71	Archaeal homoheptameric Sm protein {Archaeon Pyroc	99.93
d1mgqa_	74	Archaeal homoheptameric Sm protein {Archaeon Metha	99.93
d1i8fa_	71	Archaeal homoheptameric Sm protein {Archaeon Pyrob	99.92
d1ljoa_	75	Archaeal homoheptameric Sm protein {Archaeon Archa	99.92
d1th7a1	76	Archaeal homoheptameric Sm protein {Sulfolobus sol	99.92
d1b34a_	80	D1 core SNRNP protein {Human (Homo sapiens) [TaxId	99.92
d1n9ra_	68	Small nuclear ribonucleoprotein F, Smf {Baker's ye	99.91
d2fwka1	92	U6 snRNA-associated sm-like protein LSM5 {Cryptosp	99.87
d1b34b_	93	D2 core SNRNP protein {Human (Homo sapiens) [TaxId	99.85
d1d3bb_	81	B core SNRNP protein {Human (Homo sapiens) [TaxId:	99.85
d1m5q1_	127	Sm-Like archaeal protein Smap3 {Archaeon Pyrobacul	99.84
d2vxfa1	80	LSM14 homolog A (Lsm14a) {Zebrafish (Danio rerio)	97.35
d1biaa2	47	Biotin repressor/biotin holoenzyme synthetase, C-t	97.0
d1u1sa1	66	Pleiotropic translational regulator Hfq {Pseudomon	96.4
d1ycya1	66	Hypothetical protein PF1955 {Pyrococcus furiosus [	96.07
d1kq1a_	60	Pleiotropic translational regulator Hfq {Staphyloc	95.63
d1ib8a1	74	Hypothetical protein SP14.3 (SP0552) {Streptococcu	93.73
d2qqra1	59	Jumonji domain-containing protein 2A {Human (Homo	89.1
d1sg5a1	86	Inhibitor of Rho Rof {Escherichia coli [TaxId: 562	87.13
d2grea1	113	Deblocking aminopeptidase YhfE {Bacillus cereus [T	81.93

>d1d3ba_ b.38.1.1 (A:) D3 core SNRNP protein {Human (Homo sapiens) [TaxId: 9606]}

class: All beta proteins
fold: Sm-like fold
superfamily: Sm-like ribonucleoproteins
family: Sm motif of small nuclear ribonucleoproteins, SNRNP
domain: D3 core SNRNP protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.94  E-value=8.6e-27  Score=138.24  Aligned_cols=71  Identities=25%  Similarity=0.431  Sum_probs=67.8

Q ss_pred             CcHHHHhhcCCCEEEEEEcCccEEEEEEEEecCCcceEEcceEEEecCeeeeeeceEEEeCCcEEEEEcCC
Q psy6372           8 NPKPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTGKLGEVLIRCNNILYIRGAE   78 (88)
Q Consensus         8 ~p~~~L~~~i~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~d~~e~~~~~~~~~~~~v~IrG~~I~~I~~~d   78 (88)
                      .|+.+|+++.|++|+|+|+||++|+|+|.+||+|||++|+||.++..++...+++.+||||++|+||++||
T Consensus         2 ~Pl~~L~~~~g~~V~VeLkng~~~~G~L~~~D~~mNi~L~~~~~~~~~~~~~~~~~v~IRG~~I~~i~lpd   72 (72)
T d1d3ba_           2 VPIKVLHEAEGHIVTCETNTGEVYRGKLIEAEDNMNCQMSNITVTYRDGRVAQLEQVYIRGCKIRFLILPD   72 (72)
T ss_dssp             CHHHHHHHTTTSEEEEEETTSCEEEEEEEEECTTCCEEEEEEEEECTTSCEEEEEEEEECGGGEEEEEECC
T ss_pred             CchHHHHhcCCCEEEEEECCCeEEEEEEEEEcCCeeEEEEEEEEEcCCCcEeEcCeEEEECCEEEEEEcCC
Confidence            69999999999999999999999999999999999999999999876667889999999999999999997

>d1i4k1_ b.38.1.1 (1:) Archaeal homoheptameric Sm protein {Archaeon Archaeoglobus fulgidus, AF-Sm1 [TaxId: 2234]}

class: All beta proteins
fold: Sm-like fold
superfamily: Sm-like ribonucleoproteins
family: Sm motif of small nuclear ribonucleoproteins, SNRNP
domain: Archaeal homoheptameric Sm protein
species: Archaeon Archaeoglobus fulgidus, AF-Sm1 [TaxId: 2234]

Probab=99.94  E-value=2e-26  Score=136.47  Aligned_cols=71  Identities=35%  Similarity=0.522  Sum_probs=67.8

Q ss_pred             CCCcHHHHhhcCCCEEEEEEcCccEEEEEEEEecCCcceEEcceEEEecCeeeeeeceEEEeCCcEEEEEc
Q psy6372           6 PCNPKPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTGKLGEVLIRCNNILYIRG   76 (88)
Q Consensus         6 ~~~p~~~L~~~i~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~d~~e~~~~~~~~~~~~v~IrG~~I~~I~~   76 (88)
                      |..|+.+|++++|++|+|+|+||++|+|+|.+||+|||++|+||+++..++..++++.+||||++|+||.+
T Consensus         1 p~~Pl~~L~~~~~~~V~V~lk~g~~~~G~L~~~D~~mNlvL~~~~e~~~~~~~~~~g~~~IRG~~I~~Isp   71 (72)
T d1i4k1_           1 PPRPLDVLNRSLKSPVIVRLKGGREFRGTLDGYDIHMNLVLLDAEEIQNGEVVRKVGSVVIRGDTVVFVSP   71 (72)
T ss_dssp             CCCHHHHHHTTTTSEEEEEEGGGCEEEEEEEEECTTCCEEEEEEEEESSSSEEEEEEEEEECGGGEEEEEC
T ss_pred             CCChHHHHHHhCCCEEEEEECCCCEEEEEEEEEcCCCCeEEeeEEEEecCCeEeEcceEEEeCCeEEEEEc
Confidence            67899999999999999999999999999999999999999999999777788999999999999999974

>d1h641_ b.38.1.1 (1:) Archaeal homoheptameric Sm protein {Archaeon Pyrococcus abyssi [TaxId: 29292]}

class: All beta proteins
fold: Sm-like fold
superfamily: Sm-like ribonucleoproteins
family: Sm motif of small nuclear ribonucleoproteins, SNRNP
domain: Archaeal homoheptameric Sm protein
species: Archaeon Pyrococcus abyssi [TaxId: 29292]

Probab=99.93  E-value=4.3e-26  Score=134.58  Aligned_cols=70  Identities=33%  Similarity=0.477  Sum_probs=67.1

Q ss_pred             CCcHHHHhhcCCCEEEEEEcCccEEEEEEEEecCCcceEEcceEEEecCeeeeeeceEEEeCCcEEEEEc
Q psy6372           7 CNPKPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTGKLGEVLIRCNNILYIRG   76 (88)
Q Consensus         7 ~~p~~~L~~~i~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~d~~e~~~~~~~~~~~~v~IrG~~I~~I~~   76 (88)
                      ..|+++|++++|++|+|+|+||++|+|+|.+||+|||++|+||.+..+++..++++.+||||++|+||++
T Consensus         1 ~~Pl~~L~~~~~~~V~V~lk~g~~~~G~L~~~D~~mNlvL~~~~e~~~~~~~~~l~~~~IRG~~I~~Isp   70 (71)
T d1h641_           1 ERPLDVIHRSLDKDVLVILKKGFEFRGRLIGYDIHLNVVLADAEMIQDGEVVKRYGKIVIRGDNVLAISP   70 (71)
T ss_dssp             CCHHHHHHTTTTSEEEEEETTSEEEEEEEEEECTTCCEEEEEEEEEETTEEEEEEEEEEECGGGEEEEEE
T ss_pred             CCchHHHHHhCCCEEEEEEcCCCEEEEEEEEECCCCCeEEeeEEEEecCCcEeEcCcEEEECCeEEEEeC
Confidence            3699999999999999999999999999999999999999999999888889999999999999999986

>d1mgqa_ b.38.1.1 (A:) Archaeal homoheptameric Sm protein {Archaeon Methanobacterium thermoautotrophicum [TaxId: 145262]}

class: All beta proteins
fold: Sm-like fold
superfamily: Sm-like ribonucleoproteins
family: Sm motif of small nuclear ribonucleoproteins, SNRNP
domain: Archaeal homoheptameric Sm protein
species: Archaeon Methanobacterium thermoautotrophicum [TaxId: 145262]

Probab=99.93  E-value=9.2e-26  Score=134.24  Aligned_cols=72  Identities=42%  Similarity=0.505  Sum_probs=68.4

Q ss_pred             CCCCcHHHHhhcCCCEEEEEEcCccEEEEEEEEecCCcceEEcceEEEecCeeeeeeceEEEeCCcEEEEEc
Q psy6372           5 LPCNPKPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTGKLGEVLIRCNNILYIRG   76 (88)
Q Consensus         5 ~~~~p~~~L~~~i~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~d~~e~~~~~~~~~~~~v~IrG~~I~~I~~   76 (88)
                      ....|+++|++++|++|.|+|+||+.|+|+|.+||+|||++|+||++..+++..++++.+||||++|+||.+
T Consensus         3 ~~~~Pl~~L~~~~~k~V~V~lk~g~~~~G~L~~~D~~mNl~L~~~~e~~~~~~~~~~~~~~IRG~~I~~I~p   74 (74)
T d1mgqa_           3 NVQRPLDALGNSLNSPVIIKLKGDREFRGVLKSFDLHMNLVLNDAEELEDGEVTRRLGTVLIRGDNIVYISP   74 (74)
T ss_dssp             CTTCTTHHHHHTTTSEEEEEETTTEEEEEEEEEECTTCCEEEEEEEEEETTEEEEEEEEEEECGGGEEEEEC
T ss_pred             cccCcHHHHHHhCCCeEEEEECCCCEEEEEEEEECCCCCeEEeeEEEEeCCCeEeEcceEEEeCCEEEEEeC
Confidence            456799999999999999999999999999999999999999999999888889999999999999999974

>d1i8fa_ b.38.1.1 (A:) Archaeal homoheptameric Sm protein {Archaeon Pyrobaculum aerophilum [TaxId: 13773]}

class: All beta proteins
fold: Sm-like fold
superfamily: Sm-like ribonucleoproteins
family: Sm motif of small nuclear ribonucleoproteins, SNRNP
domain: Archaeal homoheptameric Sm protein
species: Archaeon Pyrobaculum aerophilum [TaxId: 13773]

Probab=99.92  E-value=5.5e-25  Score=130.16  Aligned_cols=70  Identities=39%  Similarity=0.495  Sum_probs=65.0

Q ss_pred             CcHHHHhhcCCCEEEEEEcCccEEEEEEEEecCCcceEEcceEEEecCeeeeeeceEEEeCCcEEEEEcCC
Q psy6372           8 NPKPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTGKLGEVLIRCNNILYIRGAE   78 (88)
Q Consensus         8 ~p~~~L~~~i~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~d~~e~~~~~~~~~~~~v~IrG~~I~~I~~~d   78 (88)
                      ++.++|++++||+|+|+|+||+.|.|+|.+||+|||++|+||.+...+ +.++++.+||||++|+||.+++
T Consensus         2 t~~~~L~~~~~k~V~V~Lk~g~~~~G~L~~~D~~mNivL~~~~e~~~~-~~~~~g~v~iRG~~I~~I~~~P   71 (71)
T d1i8fa_           2 TLGATLQDSIGKQVLVKLRDSHEIRGILRSFDQHVNLLLEDAEEIIDG-NVYKRGTMVVRGENVLFISPVP   71 (71)
T ss_dssp             CHHHHHHTTTTSEEEEEEGGGEEEEEEEEEECTTCCEEEEEEEEEETT-EEEEEEEEEECGGGEEEEEECC
T ss_pred             cHhHHHHHhCCCEEEEEECCCCEEEEEEEEECCCcceEEccEEEEECC-CEEEcceEEEeCCeEEEEeCCC
Confidence            467899999999999999999999999999999999999999998776 4788999999999999998764

>d1ljoa_ b.38.1.1 (A:) Archaeal homoheptameric Sm protein {Archaeon Archaeoglobus fulgidus, AF-Sm2 [TaxId: 2234]}

class: All beta proteins
fold: Sm-like fold
superfamily: Sm-like ribonucleoproteins
family: Sm motif of small nuclear ribonucleoproteins, SNRNP
domain: Archaeal homoheptameric Sm protein
species: Archaeon Archaeoglobus fulgidus, AF-Sm2 [TaxId: 2234]

Probab=99.92  E-value=5.8e-25  Score=131.32  Aligned_cols=70  Identities=27%  Similarity=0.422  Sum_probs=66.4

Q ss_pred             CCcHHHHhhcCCCEEEEEEcCc-cEEEEEEEEecCCcceEEcceEEEecCeeeeeeceEEEeCCcEEEEEc
Q psy6372           7 CNPKPFLNLLTGKSVICKLKWG-HEYKGILVSTDGYMNCQLASTEEIIDGHCTGKLGEVLIRCNNILYIRG   76 (88)
Q Consensus         7 ~~p~~~L~~~i~k~V~V~L~~g-~~~~G~L~~~D~~mNlvL~d~~e~~~~~~~~~~~~v~IrG~~I~~I~~   76 (88)
                      ..|+.+|++++|++|+|+|++| +.|.|+|.+||+|||++|+||.+...+...++++.+||||++|+||.+
T Consensus         4 ~~P~~~L~~~~~~~V~V~lk~~~~~~~G~L~~~D~~mNlvL~~~~e~~~~~~~~~~g~~~IRG~~I~~I~p   74 (75)
T d1ljoa_           4 VLPNQMVKSMVGKIIRVEMKGEENQLVGKLEGVDDYMNLYLTNAMECKGEEKVRSLGEIVLRGNNVVLIQP   74 (75)
T ss_dssp             CCHHHHHHHTTTSEEEEEETTCSSEEEEEEEEECTTCCEEEEEEEEEETTEEEEEEEEEEECGGGEEEEEE
T ss_pred             cccHHHHHHhcCCEEEEEEECCCEEEEEEEEEEcCCCcEEEeEEEEEcCCCcEeEcceEEEeCCEEEEEEC
Confidence            5799999999999999999976 799999999999999999999999888889999999999999999985

>d1th7a1 b.38.1.1 (A:3-78) Archaeal homoheptameric Sm protein {Sulfolobus solfataricus [TaxId: 2287]}

class: All beta proteins
fold: Sm-like fold
superfamily: Sm-like ribonucleoproteins
family: Sm motif of small nuclear ribonucleoproteins, SNRNP
domain: Archaeal homoheptameric Sm protein
species: Sulfolobus solfataricus [TaxId: 2287]

Probab=99.92  E-value=2.4e-25  Score=133.11  Aligned_cols=74  Identities=32%  Similarity=0.385  Sum_probs=68.5

Q ss_pred             CCCCCCcHHHHhhcCCCEEEEEEcCccEEEEEEEEecCCcceEEcceEEEecCeeeeeeceEEEeCCcEEEEEc
Q psy6372           3 TPLPCNPKPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTGKLGEVLIRCNNILYIRG   76 (88)
Q Consensus         3 ~~~~~~p~~~L~~~i~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~d~~e~~~~~~~~~~~~v~IrG~~I~~I~~   76 (88)
                      +..+..|.++|++++|++|+|+|+||++|+|+|.+||+|||++|+||+++..+...+.++.+||||++|++|.+
T Consensus         2 ~~~~~~~~~~L~~~~~~~V~V~lk~g~~~~G~L~~~D~~mNlvL~~~~e~~~~~~~~~~~~v~iRG~~I~~I~~   75 (76)
T d1th7a1           2 NFLAETAHKVLAESLNNLVLVKLKGNKEVRGMLRSYDQHMNLVLSDSEEIQSDGSGKKLGTIVIRGDNVILISP   75 (76)
T ss_dssp             CTTCHHHHHHHHHHTTSEEEEEETTTEEEEEEEEEECTTCCEEEEEEEEECSSSCEEEEEEEEECGGGEEEEEE
T ss_pred             CcccccHHHHHHHhCCCEEEEEECCCCEEEEEEEEECCCCCEEEeEEEEEecCCcccCcceEEEECCEEEEEEe
Confidence            34456699999999999999999999999999999999999999999998777778999999999999999986

>d1b34a_ b.38.1.1 (A:) D1 core SNRNP protein {Human (Homo sapiens) [TaxId: 9606]}

class: All beta proteins
fold: Sm-like fold
superfamily: Sm-like ribonucleoproteins
family: Sm motif of small nuclear ribonucleoproteins, SNRNP
domain: D1 core SNRNP protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.92  E-value=7.8e-25  Score=132.15  Aligned_cols=72  Identities=26%  Similarity=0.299  Sum_probs=67.5

Q ss_pred             HHHHhhcCCCEEEEEEcCccEEEEEEEEecCCcceEEcceEEEecCeeeeeeceEEEeCCcEEEEEcCCCCC
Q psy6372          10 KPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTGKLGEVLIRCNNILYIRGAEEGD   81 (88)
Q Consensus        10 ~~~L~~~i~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~d~~e~~~~~~~~~~~~v~IrG~~I~~I~~~d~~~   81 (88)
                      ..||+++.|++|+|+|+||.+|+|+|.++|+|||++|+||++...++...+++.+||||++|+||++||.-+
T Consensus         3 v~fL~~~~g~~V~VeLkng~~~~G~L~~~D~~MNl~L~~~~~~~~~~~~~~~~~v~IRG~~Ir~i~lPd~l~   74 (80)
T d1b34a_           3 VRFLMKLSHETVTIELKNGTQVHGTITGVDVSMNTHLKAVKMTLKNREPVQLETLSIRGNNIRYFILPDSLP   74 (80)
T ss_dssp             HHHHHTCTTCEEEEEETTCCEEEEEEEEECTTCCEEEEEEEEECTTSCCEEEEEEEECGGGEEEEECCTTCC
T ss_pred             HHHHHHcCCCEEEEEECCCCEEEEEEEEEcCCcEEEEEEEEEEcCCCCEEEcccEEEcCCEEEEEECCCCcc
Confidence            579999999999999999999999999999999999999999877667889999999999999999998753

>d1n9ra_ b.38.1.1 (A:) Small nuclear ribonucleoprotein F, Smf {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: All beta proteins
fold: Sm-like fold
superfamily: Sm-like ribonucleoproteins
family: Sm motif of small nuclear ribonucleoproteins, SNRNP
domain: Small nuclear ribonucleoprotein F, Smf
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=99.91  E-value=9.9e-25  Score=128.15  Aligned_cols=66  Identities=52%  Similarity=0.792  Sum_probs=61.0

Q ss_pred             HhhcCCCEEEEEEc-CccEEEEEEEEecCCcceEEcceEEEecCeeeeeeceEEEeCCcEEEEE-cCC
Q psy6372          13 LNLLTGKSVICKLK-WGHEYKGILVSTDGYMNCQLASTEEIIDGHCTGKLGEVLIRCNNILYIR-GAE   78 (88)
Q Consensus        13 L~~~i~k~V~V~L~-~g~~~~G~L~~~D~~mNlvL~d~~e~~~~~~~~~~~~v~IrG~~I~~I~-~~d   78 (88)
                      |++++|++|.|+|+ +|++|+|+|.+||+|||++|+||++..+++..++++.+||||++|+||. +||
T Consensus         1 L~~~~~~~V~V~Lk~~~~~~~G~L~~~D~~mNlvL~~~~e~~~~~~~~~lg~~~IRG~nI~~I~~~pd   68 (68)
T d1n9ra_           1 LKGLVNHRVGVKLKFNSTEYRGTLVSTDNYFNLQLNEAEEFVAGVSHGTLGEIFIRCNNVLYIRELPN   68 (68)
T ss_dssp             CGGGTTSEEEEEESSTTEEEEEEEEECCTTTCEEEEEEEEEETTEEEEECCSEEECGGGEEEEEECCC
T ss_pred             ChhHCCCEEEEEEEcCCEEEEEEEEEECCcCceEEeeEEEEecCCcccCcCeEEEECCEEEEEEeCCC
Confidence            67899999999999 5678999999999999999999999988888999999999999999997 554

>d2fwka1 b.38.1.1 (A:24-115) U6 snRNA-associated sm-like protein LSM5 {Cryptosporidium parvum [TaxId: 5807]}

class: All beta proteins
fold: Sm-like fold
superfamily: Sm-like ribonucleoproteins
family: Sm motif of small nuclear ribonucleoproteins, SNRNP
domain: U6 snRNA-associated sm-like protein LSM5
species: Cryptosporidium parvum [TaxId: 5807]

Probab=99.87  E-value=5e-23  Score=126.61  Aligned_cols=70  Identities=21%  Similarity=0.319  Sum_probs=63.6

Q ss_pred             CCcHHHHhhcCCCEEEEEEcCccEEEEEEEEecCCcceEEcceEEEec---------------CeeeeeeceEEEeCCcE
Q psy6372           7 CNPKPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIID---------------GHCTGKLGEVLIRCNNI   71 (88)
Q Consensus         7 ~~p~~~L~~~i~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~d~~e~~~---------------~~~~~~~~~v~IrG~~I   71 (88)
                      ..|+++|++++||+|+|.|++|+.|.|+|.+||+|||++|+||.|+..               ....+++|++||||++|
T Consensus         4 ~~Pl~~L~~~l~k~V~V~l~~gr~~~G~L~~~D~~~NlvL~d~~E~~~~~~~~~~~~~~~~~~~~~~r~lg~~~iRG~~V   83 (92)
T d2fwka1           4 ILPLALIDKCIGNRIYVVMKGDKEFSGVLRGFDEYVNMVLDDVQEYGFKADEEDISGGNKKLKRVMVNRLETILLSGNNV   83 (92)
T ss_dssp             CCHHHHHHHTBTSBCEEEETTTEEECCEEEEECTTCCEEEESCCEEEC---------------CEECCCCSEEEECGGGE
T ss_pred             cChHHHHHHHcCCEEEEEEcCCCEEEEEEEEEcCCCCEEEeeEEEEEecCCccccccccccccccceeEcceEEEeCCEE
Confidence            579999999999999999999999999999999999999999998741               12467899999999999


Q ss_pred             EEEEc
Q psy6372          72 LYIRG   76 (88)
Q Consensus        72 ~~I~~   76 (88)
                      ++|.+
T Consensus        84 v~I~p   88 (92)
T d2fwka1          84 AMLVP   88 (92)
T ss_dssp             EEEES
T ss_pred             EEEEe
Confidence            99985

>d1b34b_ b.38.1.1 (B:) D2 core SNRNP protein {Human (Homo sapiens) [TaxId: 9606]}

class: All beta proteins
fold: Sm-like fold
superfamily: Sm-like ribonucleoproteins
family: Sm motif of small nuclear ribonucleoproteins, SNRNP
domain: D2 core SNRNP protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.85  E-value=1.5e-21  Score=120.50  Aligned_cols=72  Identities=13%  Similarity=0.184  Sum_probs=62.9

Q ss_pred             CcHHHHhhcC--CCEEEEEEcCccEEEEEEEEecCCcceEEcceEEEecC--------------eeeeeeceEEEeCCcE
Q psy6372           8 NPKPFLNLLT--GKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDG--------------HCTGKLGEVLIRCNNI   71 (88)
Q Consensus         8 ~p~~~L~~~i--~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~d~~e~~~~--------------~~~~~~~~v~IrG~~I   71 (88)
                      .|+++|..++  +++|+|.|++|+.+.|+|.+||+|||++|+||.|.+..              ...++++.+||||++|
T Consensus         2 GPl~~l~~~~~~~~rV~V~lr~~r~~~G~L~afD~~~NlVL~d~~E~~~~~~~~~~~~~~~~~~~~~R~lg~~liRGdnV   81 (93)
T d1b34b_           2 GPLSVLTQSVKNNTQVLINCRNNKKLLGRVKAFDRHCNMVLENVKEMWTEVPKSGKGKKKSKPVNKDRYISKMFLRGDSV   81 (93)
T ss_dssp             CHHHHHHHHHHHTCEEEEEETTSCEEEEEEEEECTTCCEEEEEEEEC-------------------CEEEEEEEECGGGE
T ss_pred             CcHHHHHHHHhCCcEEEEEECCCCEEEEEEEEeccceeEEeeceEEEEEecCCccccccccccceeEEEeceEEEeCCEE
Confidence            6999999998  89999999999999999999999999999999996420              1357899999999999


Q ss_pred             EEEEcCCC
Q psy6372          72 LYIRGAEE   79 (88)
Q Consensus        72 ~~I~~~d~   79 (88)
                      ++|..++.
T Consensus        82 v~I~~~p~   89 (93)
T d1b34b_          82 IVVLRNPL   89 (93)
T ss_dssp             EEEEECCC
T ss_pred             EEEEcChh
Confidence            99987764

>d1d3bb_ b.38.1.1 (B:) B core SNRNP protein {Human (Homo sapiens) [TaxId: 9606]}

class: All beta proteins
fold: Sm-like fold
superfamily: Sm-like ribonucleoproteins
family: Sm motif of small nuclear ribonucleoproteins, SNRNP
domain: B core SNRNP protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.85  E-value=1.7e-21  Score=117.31  Aligned_cols=66  Identities=23%  Similarity=0.248  Sum_probs=58.8

Q ss_pred             HHhhcCCCEEEEEEcCccEEEEEEEEecCCcceEEcceEEEec----------CeeeeeeceEEEeCCcEEEEEcC
Q psy6372          12 FLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIID----------GHCTGKLGEVLIRCNNILYIRGA   77 (88)
Q Consensus        12 ~L~~~i~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~d~~e~~~----------~~~~~~~~~v~IrG~~I~~I~~~   77 (88)
                      -|.+++|++|+|.|+|||.|.|+|.+||+||||+|+||.|++.          ....+.+|+++|||++|++|.+.
T Consensus         2 ~L~~~l~~rv~V~l~dgR~~~G~L~~~D~~~NlvL~~~~E~~~~~~~~~~~~~~~~~r~lG~v~IRG~~Iv~i~~~   77 (81)
T d1d3bb_           2 KMLQHIDYRMRCILQDGRIFIGTFKAFDKHMNLILCDCDEFRKIKPKNSKQAEREEKRVLGLVLLRGENLVSMTVE   77 (81)
T ss_dssp             CCGGGTTSEEEEEETTCCEEEEEEEECCTTCCEEEEEEEEEEEECCSSTTSCCEEEEEEEEEEEECGGGEEEEEEE
T ss_pred             hhHHHCCCEEEEEEcCCCEEEEEEEEECCccCEEEcCEEEEEeecCccccccccceEEEeeeEEEeCCEEEEEEcc
Confidence            3788999999999999999999999999999999999999741          12568899999999999999853

>d1m5q1_ b.38.1.1 (1:) Sm-Like archaeal protein Smap3 {Archaeon Pyrobaculum aerophilum [TaxId: 13773]}

class: All beta proteins
fold: Sm-like fold
superfamily: Sm-like ribonucleoproteins
family: Sm motif of small nuclear ribonucleoproteins, SNRNP
domain: Sm-Like archaeal protein Smap3
species: Archaeon Pyrobaculum aerophilum [TaxId: 13773]

Probab=99.84  E-value=3.7e-21  Score=124.67  Aligned_cols=69  Identities=32%  Similarity=0.400  Sum_probs=62.5

Q ss_pred             HHHHhhcCCCEEEEEEcCccEEEEEEEEecCCcceEEcceEEEecCeeeeeeceEEEeCCcEEEEEcCCCCCc
Q psy6372          10 KPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTGKLGEVLIRCNNILYIRGAEEGDE   82 (88)
Q Consensus        10 ~~~L~~~i~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~d~~e~~~~~~~~~~~~v~IrG~~I~~I~~~d~~~~   82 (88)
                      +++|++++|++|.|+|+||++|+|+|.+||+|||++|+||++.. +   .+++.++|||++|+||.+|++..+
T Consensus         2 ~~~L~~~~gk~V~VeLkng~~~~G~L~~~D~~mNivL~da~~~~-~---~k~~~v~IRG~~I~~I~~~e~~iD   70 (127)
T d1m5q1_           2 VAELNNLLGREVQVVLSNGEVYKGVLHAVDNQLNIVLANASNKA-G---EKFNRVFIMYRYIVHIDSTERRID   70 (127)
T ss_dssp             HHHHHTTTTSEEEEEETTSCEEEEEEEEECTTCCEEEEEEEETT-C---CEEEEEEECGGGEEEEEECSCCCC
T ss_pred             hhHHHHhCCCEEEEEECCCCEEEEEEEEECCCceEEEeEEEECC-C---CcccEEEEeCCeEEEEEcchhhcC
Confidence            57899999999999999999999999999999999999999752 2   357889999999999999998654

>d2vxfa1 b.38.1.5 (A:6-85) LSM14 homolog A (Lsm14a) {Zebrafish (Danio rerio) [TaxId: 7955]}

class: All beta proteins
fold: Sm-like fold
superfamily: Sm-like ribonucleoproteins
family: LSM14 N-terminal domain-like
domain: LSM14 homolog A (Lsm14a)
species: Zebrafish (Danio rerio) [TaxId: 7955]

Probab=97.35  E-value=0.00098  Score=38.69  Aligned_cols=63  Identities=19%  Similarity=0.232  Sum_probs=52.2

Q ss_pred             cCCCEEEEEEcCccEEEEEEEEec-CCcceEEcceEEE-ecC--------eeeeeeceEEEeCCcEEEEEcCC
Q psy6372          16 LTGKSVICKLKWGHEYKGILVSTD-GYMNCQLASTEEI-IDG--------HCTGKLGEVLIRCNNILYIRGAE   78 (88)
Q Consensus        16 ~i~k~V~V~L~~g~~~~G~L~~~D-~~mNlvL~d~~e~-~~~--------~~~~~~~~v~IrG~~I~~I~~~d   78 (88)
                      ++|+++.+..+.+-.|.|+|..+| +..-+.|+|+..+ .+|        ....-++.+..||+.|.-+.+.+
T Consensus         2 yIGs~IsLISk~dIRYeGiL~~Id~~~sTi~L~nVrsfGTEgR~~~~~ipp~~~vy~~IvFrgsDIKdL~v~e   74 (80)
T d2vxfa1           2 YIGSKISLISKAEIRYEGILYTIDTENSTVALAKVRSFGTEDRPTDRPIAPRDETFEYIIFRGSDIKDLTVCE   74 (80)
T ss_dssp             STTSEEEEEETTSCEEEEEEEEEETTTTEEEEEEEEECCSTTSCCSSCCCCCCCCEEEEEEETTTEEEEEESS
T ss_pred             ccCCEEEEEEcCCcEEEEEEEeeccccCEEEeeeeeEeecCCCCCCCccCCCCcceeEEEEcCcCcceEEecc
Confidence            689999999999999999999999 4567999999875 221        13456789999999999988754

>d1biaa2 b.34.1.1 (A:271-317) Biotin repressor/biotin holoenzyme synthetase, C-terminal domain {Escherichia coli [TaxId: 562]}

class: All beta proteins
fold: SH3-like barrel
superfamily: C-terminal domain of transcriptional repressors
family: Biotin repressor (BirA)
domain: Biotin repressor/biotin holoenzyme synthetase, C-terminal domain
species: Escherichia coli [TaxId: 562]

Probab=97.00  E-value=0.0015  Score=34.01  Aligned_cols=47  Identities=21%  Similarity=0.121  Sum_probs=35.0

Q ss_pred             cCCCEEEEEEcCccEEEEEEEEecCCcceEEcceEEEecCeeeeeeceEEEe
Q psy6372          16 LTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTGKLGEVLIR   67 (88)
Q Consensus        16 ~i~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~d~~e~~~~~~~~~~~~v~Ir   67 (88)
                      |+||+|+|..- ++++.|+..++|+.-.|.|+.....    ....-|.+.||
T Consensus         1 f~gk~V~v~~g-~~~i~G~a~gId~~G~Lll~t~~g~----~~~~sGEVSlR   47 (47)
T d1biaa2           1 FINRPVKLIIG-DKEIFGISRGIDKQGALLLEQDGII----KPWMGGEISLR   47 (47)
T ss_dssp             TTTSEEEEEET-TEEEEEEEEEECTTSCEEEEETTEE----EEESSCEEEEC
T ss_pred             CCCCEEEEEEC-CeEEEEEEeeECCCCcEEEEECCCE----EEEEEEEEEeC
Confidence            68999999764 5789999999999999998643322    33444666665

>d1u1sa1 b.38.1.2 (A:6-71) Pleiotropic translational regulator Hfq {Pseudomonas aeruginosa [TaxId: 287]}

class: All beta proteins
fold: Sm-like fold
superfamily: Sm-like ribonucleoproteins
family: Pleiotropic translational regulator Hfq
domain: Pleiotropic translational regulator Hfq
species: Pseudomonas aeruginosa [TaxId: 287]

Probab=96.40  E-value=0.0042  Score=34.66  Aligned_cols=36  Identities=31%  Similarity=0.374  Sum_probs=29.0

Q ss_pred             HHHhhc--CCCEEEEEEcCccEEEEEEEEecCCcceEEc
Q psy6372          11 PFLNLL--TGKSVICKLKWGHEYKGILVSTDGYMNCQLA   47 (88)
Q Consensus        11 ~~L~~~--i~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~   47 (88)
                      .||..+  -..+|+|-|.||-.++|.+.+||+|.= .|+
T Consensus         5 ~fLn~~rk~~~~VtifL~nGvkl~G~I~~fD~ftv-LL~   42 (66)
T d1u1sa1           5 PYLNTLRKERVPVSIYLVNGIKLQGQIESFDQFVI-LLK   42 (66)
T ss_dssp             HHHHHHHHTTCCEEEEETTSCEEEEEEEEECSSEE-EEE
T ss_pred             HHHHHHHHcCCcEEEEEEcCcEEEEEEEEEcceEE-EEE
Confidence            355555  367799999999999999999999974 443

>d1ycya1 b.38.1.4 (A:5-70) Hypothetical protein PF1955 {Pyrococcus furiosus [TaxId: 2261]}

class: All beta proteins
fold: Sm-like fold
superfamily: Sm-like ribonucleoproteins
family: PF1955-like
domain: Hypothetical protein PF1955
species: Pyrococcus furiosus [TaxId: 2261]

Probab=96.07  E-value=0.021  Score=31.23  Aligned_cols=59  Identities=24%  Similarity=0.361  Sum_probs=41.0

Q ss_pred             HHHhhcCCCEEEEEEcCccEEEEEEEEecCCcceEEcceEEEecCeeeeeeceEEEeCCcEEEE
Q psy6372          11 PFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTGKLGEVLIRCNNILYI   74 (88)
Q Consensus        11 ~~L~~~i~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~d~~e~~~~~~~~~~~~v~IrG~~I~~I   74 (88)
                      ..|..-.|++|-|.......++|+|..||.-. +.|+|++... |+   +-..++++=+.|-.|
T Consensus         5 ktL~~WKg~kvAv~vgsehSFtGiledFDeEv-iLL~dV~D~~-GN---k~k~llv~idD~nWi   63 (66)
T d1ycya1           5 KVLKEWKGHKVAVSVGGDHSFTGTLEDFDEEV-ILLKDVVDVI-GN---RGKQMLIGLEDINWI   63 (66)
T ss_dssp             HHHHHHTTSEEEEEEC----CEEEEEEECSSE-EEEEEEEETT-EE---EEEEEEEEGGGEEEE
T ss_pred             HHHHHhCCcEEEEEecCcceeEEEhhhcCcce-EeehhhHHHh-cc---ccceeEEEeccceeE
Confidence            46788899999999999999999999999987 7889999762 22   223455655555544

>d1kq1a_ b.38.1.2 (A:) Pleiotropic translational regulator Hfq {Staphylococcus aureus [TaxId: 1280]}

class: All beta proteins
fold: Sm-like fold
superfamily: Sm-like ribonucleoproteins
family: Pleiotropic translational regulator Hfq
domain: Pleiotropic translational regulator Hfq
species: Staphylococcus aureus [TaxId: 1280]

Probab=95.63  E-value=0.015  Score=31.75  Aligned_cols=37  Identities=19%  Similarity=0.222  Sum_probs=29.8

Q ss_pred             HHhhcC--CCEEEEEEcCccEEEEEEEEecCCcceEEcc
Q psy6372          12 FLNLLT--GKSVICKLKWGHEYKGILVSTDGYMNCQLAS   48 (88)
Q Consensus        12 ~L~~~i--~k~V~V~L~~g~~~~G~L~~~D~~mNlvL~d   48 (88)
                      ||..+.  ..+|+|-|.||-.++|.+.+||+|.=+...+
T Consensus         6 fln~lr~~~~~VtifL~nGvkl~G~I~~fD~ftvlL~~~   44 (60)
T d1kq1a_           6 ALENFKANQTEVTVFFLNGFQMKGVIEEYDKYVVSLNSQ   44 (60)
T ss_dssp             HHHHHHHHTCEEEEEETTSCEEEEEEEEECSSEEEEEET
T ss_pred             HHHHHHHcCCcEEEEEECCcEEEEEEEEEcceEEEEEeC
Confidence            555553  6789999999999999999999998555443

>d1ib8a1 b.38.2.1 (A:91-164) Hypothetical protein SP14.3 (SP0552) {Streptococcus pneumoniae [TaxId: 1313]}

class: All beta proteins
fold: Sm-like fold
superfamily: YhbC-like, C-terminal domain
family: YhbC-like, C-terminal domain
domain: Hypothetical protein SP14.3 (SP0552)
species: Streptococcus pneumoniae [TaxId: 1313]

Probab=93.73  E-value=0.058  Score=29.75  Aligned_cols=35  Identities=17%  Similarity=0.151  Sum_probs=28.5

Q ss_pred             CcHHHHhhcCCCEEEEEEcC---c-cEEEEEEEEecCCc
Q psy6372           8 NPKPFLNLLTGKSVICKLKW---G-HEYKGILVSTDGYM   42 (88)
Q Consensus         8 ~p~~~L~~~i~k~V~V~L~~---g-~~~~G~L~~~D~~m   42 (88)
                      .-..-+..++|+.|.|+|+.   | +.++|+|.++|+..
T Consensus         4 ~~~~~f~r~~G~~v~v~l~~p~~g~k~f~G~L~~~~~~~   42 (74)
T d1ib8a1           4 KTKDAVAGAVGKYIHVGLYQAIDKQKVFEGTLLAFEEDE   42 (74)
T ss_dssp             SSHHHHHHHCSEEEEEECSSCSSSCSEEEEEEEEEETTE
T ss_pred             CCHHHHHHhCCCEEEEEEecccCCceEEEEEEEeecCCe
Confidence            33456788999999999953   3 89999999999864

>d2qqra1 b.34.9.1 (A:897-955) Jumonji domain-containing protein 2A {Human (Homo sapiens) [TaxId: 9606]}

class: All beta proteins
fold: SH3-like barrel
superfamily: Tudor/PWWP/MBT
family: Tudor domain
domain: Jumonji domain-containing protein 2A
species: Human (Homo sapiens) [TaxId: 9606]

Probab=89.10  E-value=0.3  Score=26.17  Aligned_cols=24  Identities=33%  Similarity=0.383  Sum_probs=21.5

Q ss_pred             cCCCEEEEEEcCccEEEEEEEEec
Q psy6372          16 LTGKSVICKLKWGHEYKGILVSTD   39 (88)
Q Consensus        16 ~i~k~V~V~L~~g~~~~G~L~~~D   39 (88)
                      .+|++|.-+.+||+.|++++.+.-
T Consensus         4 ~~Gq~VI~KhkNgryY~c~V~~~~   27 (59)
T d2qqra1           4 TAGQKVISKHKNGRFYQCEVVRLT   27 (59)
T ss_dssp             CTTCEEEEECTTSSEEEEEEEEEE
T ss_pred             ccccEEEEEccCCcEEEEEEEEee
Confidence            379999999999999999998864

>d1sg5a1 b.137.1.2 (A:1-86) Inhibitor of Rho Rof {Escherichia coli [TaxId: 562]}

class: All beta proteins
fold: Rof/RNase P subunit-like
superfamily: Rof/RNase P subunit-like
family: Rof-like
domain: Inhibitor of Rho Rof
species: Escherichia coli [TaxId: 562]

Probab=87.13  E-value=0.18  Score=28.97  Aligned_cols=35  Identities=20%  Similarity=0.071  Sum_probs=28.5

Q ss_pred             CCCCCCCCcHH-------HHhhcCCCEEEEEEcCccEEEEEE
Q psy6372           1 MSTPLPCNPKP-------FLNLLTGKSVICKLKWGHEYKGIL   35 (88)
Q Consensus         1 m~~~~~~~p~~-------~L~~~i~k~V~V~L~~g~~~~G~L   35 (88)
                      ||...+..|++       .+..+.+.++.++|+||..+.|+-
T Consensus         1 m~m~~~Y~pI~C~~yDyLEiaC~~~~~l~l~l~dG~~~~g~a   42 (86)
T d1sg5a1           1 MSMNDTYQPINCDDYDNLELACQHHLMLTLELKDGEKLQAKA   42 (86)
T ss_dssp             CCCCCCCCSSCCSSHHHHHHHHTTTTCEEEECTTTCCEEESS
T ss_pred             CCCCCCccccccchhhHHHHHHHcCCcEEEEEeCCCEEEEEE
Confidence            67777777763       567778999999999999999943

>d2grea1 b.49.3.1 (A:74-186) Deblocking aminopeptidase YhfE {Bacillus cereus [TaxId: 1396]}

class: All beta proteins
fold: Domain of alpha and beta subunits of F1 ATP synthase-like
superfamily: Aminopeptidase/glucanase lid domain
family: Aminopeptidase/glucanase lid domain
domain: Deblocking aminopeptidase YhfE
species: Bacillus cereus [TaxId: 1396]

Probab=81.93  E-value=0.73  Score=27.13  Aligned_cols=24  Identities=21%  Similarity=0.368  Sum_probs=20.9

Q ss_pred             hhcCCCEEEEEEcCccEEEEEEEE
Q psy6372          14 NLLTGKSVICKLKWGHEYKGILVS   37 (88)
Q Consensus        14 ~~~i~k~V~V~L~~g~~~~G~L~~   37 (88)
                      +.+.+++|+|.+++|+.|.|++-+
T Consensus        24 ~~l~gq~V~I~t~~G~~i~Gvig~   47 (113)
T d2grea1          24 NSVEGEYCEIETSSGKTYTGTILM   47 (113)
T ss_dssp             GGTTTCEEEEECTTSCEEEEEEEC
T ss_pred             hhcccCEEEEEcCCCCEEEEEEec
Confidence            456899999999999999999753